diff --git a/src/tint/fuzzers/shuffle_transform.cc b/src/tint/fuzzers/shuffle_transform.cc
index 5f5f6e6..6ae405a 100644
--- a/src/tint/fuzzers/shuffle_transform.cc
+++ b/src/tint/fuzzers/shuffle_transform.cc
@@ -15,6 +15,7 @@
 #include "src/tint/fuzzers/shuffle_transform.h"
 
 #include <random>
+#include <utility>
 
 #include "src/tint/program_builder.h"
 
@@ -22,15 +23,21 @@
 
 ShuffleTransform::ShuffleTransform(size_t seed) : seed_(seed) {}
 
-void ShuffleTransform::Run(CloneContext& ctx,
-                           const tint::transform::DataMap&,
-                           tint::transform::DataMap&) const {
-    auto decls = ctx.src->AST().GlobalDeclarations();
+transform::Transform::ApplyResult ShuffleTransform::Apply(const Program* src,
+                                                          const transform::DataMap&,
+                                                          transform::DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
+    auto decls = src->AST().GlobalDeclarations();
     auto rng = std::mt19937_64{seed_};
     std::shuffle(std::begin(decls), std::end(decls), rng);
     for (auto* decl : decls) {
-        ctx.dst->AST().AddGlobalDeclaration(ctx.Clone(decl));
+        b.AST().AddGlobalDeclaration(ctx.Clone(decl));
     }
+
+    ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::fuzzers
diff --git a/src/tint/fuzzers/shuffle_transform.h b/src/tint/fuzzers/shuffle_transform.h
index 0a64fe3..ee54f97 100644
--- a/src/tint/fuzzers/shuffle_transform.h
+++ b/src/tint/fuzzers/shuffle_transform.h
@@ -20,16 +20,16 @@
 namespace tint::fuzzers {
 
 /// ShuffleTransform reorders the module scope declarations into a random order
-class ShuffleTransform : public tint::transform::Transform {
+class ShuffleTransform : public transform::Transform {
   public:
     /// Constructor
     /// @param seed the random seed to use for the shuffling
     explicit ShuffleTransform(size_t seed);
 
-  protected:
-    void Run(CloneContext& ctx,
-             const tint::transform::DataMap&,
-             tint::transform::DataMap&) const override;
+    /// @copydoc transform::Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const transform::DataMap& inputs,
+                      transform::DataMap& outputs) const override;
 
   private:
     size_t seed_;
diff --git a/src/tint/sem/variable.h b/src/tint/sem/variable.h
index 8e271d7..634f5da 100644
--- a/src/tint/sem/variable.h
+++ b/src/tint/sem/variable.h
@@ -23,6 +23,7 @@
 
 #include "src/tint/ast/access.h"
 #include "src/tint/ast/address_space.h"
+#include "src/tint/ast/parameter.h"
 #include "src/tint/sem/binding_point.h"
 #include "src/tint/sem/expression.h"
 #include "src/tint/sem/parameter_usage.h"
@@ -212,6 +213,11 @@
     /// Destructor
     ~Parameter() override;
 
+    /// @returns the AST declaration node
+    const ast::Parameter* Declaration() const {
+        return static_cast<const ast::Parameter*>(Variable::Declaration());
+    }
+
     /// @return the index of the parmeter in the function
     uint32_t Index() const { return index_; }
 
diff --git a/src/tint/transform/add_block_attribute.cc b/src/tint/transform/add_block_attribute.cc
index 77d8719..513925f 100644
--- a/src/tint/transform/add_block_attribute.cc
+++ b/src/tint/transform/add_block_attribute.cc
@@ -31,21 +31,29 @@
 
 AddBlockAttribute::~AddBlockAttribute() = default;
 
-void AddBlockAttribute::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    auto& sem = ctx.src->Sem();
+Transform::ApplyResult AddBlockAttribute::Apply(const Program* src,
+                                                const DataMap&,
+                                                DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
+    auto& sem = src->Sem();
 
     // A map from a type in the source program to a block-decorated wrapper that contains it in the
     // destination program.
     utils::Hashmap<const sem::Type*, const ast::Struct*, 8> wrapper_structs;
 
     // Process global 'var' declarations that are buffers.
-    for (auto* global : ctx.src->AST().GlobalVariables()) {
+    bool made_changes = false;
+    for (auto* global : src->AST().GlobalVariables()) {
         auto* var = sem.Get(global);
         if (!ast::IsHostShareable(var->AddressSpace())) {
             // Not declared in a host-sharable address space
             continue;
         }
 
+        made_changes = true;
+
         auto* ty = var->Type()->UnwrapRef();
         auto* str = ty->As<sem::Struct>();
 
@@ -61,33 +69,36 @@
             const char* kMemberName = "inner";
 
             auto* wrapper = wrapper_structs.GetOrCreate(ty, [&] {
-                auto* block = ctx.dst->ASTNodes().Create<BlockAttribute>(ctx.dst->ID(),
-                                                                         ctx.dst->AllocateNodeID());
-                auto wrapper_name = ctx.src->Symbols().NameFor(global->symbol) + "_block";
-                auto* ret = ctx.dst->create<ast::Struct>(
-                    ctx.dst->Symbols().New(wrapper_name),
-                    utils::Vector{ctx.dst->Member(kMemberName, CreateASTTypeFor(ctx, ty))},
+                auto* block = b.ASTNodes().Create<BlockAttribute>(b.ID(), b.AllocateNodeID());
+                auto wrapper_name = src->Symbols().NameFor(global->symbol) + "_block";
+                auto* ret = b.create<ast::Struct>(
+                    b.Symbols().New(wrapper_name),
+                    utils::Vector{b.Member(kMemberName, CreateASTTypeFor(ctx, ty))},
                     utils::Vector{block});
-                ctx.InsertBefore(ctx.src->AST().GlobalDeclarations(), global, ret);
+                ctx.InsertBefore(src->AST().GlobalDeclarations(), global, ret);
                 return ret;
             });
-            ctx.Replace(global->type, ctx.dst->ty.Of(wrapper));
+            ctx.Replace(global->type, b.ty.Of(wrapper));
 
             // Insert a member accessor to get the original type from the wrapper at
             // any usage of the original variable.
             for (auto* user : var->Users()) {
                 ctx.Replace(user->Declaration(),
-                            ctx.dst->MemberAccessor(ctx.Clone(global->symbol), kMemberName));
+                            b.MemberAccessor(ctx.Clone(global->symbol), kMemberName));
             }
         } else {
             // Add a block attribute to this struct directly.
-            auto* block = ctx.dst->ASTNodes().Create<BlockAttribute>(ctx.dst->ID(),
-                                                                     ctx.dst->AllocateNodeID());
+            auto* block = b.ASTNodes().Create<BlockAttribute>(b.ID(), b.AllocateNodeID());
             ctx.InsertFront(str->Declaration()->attributes, block);
         }
     }
 
+    if (!made_changes) {
+        return SkipTransform;
+    }
+
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 AddBlockAttribute::BlockAttribute::BlockAttribute(ProgramID pid, ast::NodeID nid)
diff --git a/src/tint/transform/add_block_attribute.h b/src/tint/transform/add_block_attribute.h
index 2bfd63e..d5e8c4e 100644
--- a/src/tint/transform/add_block_attribute.h
+++ b/src/tint/transform/add_block_attribute.h
@@ -53,14 +53,10 @@
     /// Destructor
     ~AddBlockAttribute() override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/add_empty_entry_point.cc b/src/tint/transform/add_empty_entry_point.cc
index 5ef4fe8..f71394d 100644
--- a/src/tint/transform/add_empty_entry_point.cc
+++ b/src/tint/transform/add_empty_entry_point.cc
@@ -23,12 +23,9 @@
 using namespace tint::number_suffixes;  // NOLINT
 
 namespace tint::transform {
+namespace {
 
-AddEmptyEntryPoint::AddEmptyEntryPoint() = default;
-
-AddEmptyEntryPoint::~AddEmptyEntryPoint() = default;
-
-bool AddEmptyEntryPoint::ShouldRun(const Program* program, const DataMap&) const {
+bool ShouldRun(const Program* program) {
     for (auto* func : program->AST().Functions()) {
         if (func->IsEntryPoint()) {
             return false;
@@ -37,13 +34,30 @@
     return true;
 }
 
-void AddEmptyEntryPoint::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    ctx.dst->Func(ctx.dst->Symbols().New("unused_entry_point"), {}, ctx.dst->ty.void_(), {},
-                  utils::Vector{
-                      ctx.dst->Stage(ast::PipelineStage::kCompute),
-                      ctx.dst->WorkgroupSize(1_i),
-                  });
+}  // namespace
+
+AddEmptyEntryPoint::AddEmptyEntryPoint() = default;
+
+AddEmptyEntryPoint::~AddEmptyEntryPoint() = default;
+
+Transform::ApplyResult AddEmptyEntryPoint::Apply(const Program* src,
+                                                 const DataMap&,
+                                                 DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
+    }
+
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
+    b.Func(b.Symbols().New("unused_entry_point"), {}, b.ty.void_(), {},
+           utils::Vector{
+               b.Stage(ast::PipelineStage::kCompute),
+               b.WorkgroupSize(1_i),
+           });
+
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/add_empty_entry_point.h b/src/tint/transform/add_empty_entry_point.h
index 5530355..828f3b5 100644
--- a/src/tint/transform/add_empty_entry_point.h
+++ b/src/tint/transform/add_empty_entry_point.h
@@ -27,19 +27,10 @@
     /// Destructor
     ~AddEmptyEntryPoint() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/array_length_from_uniform.cc b/src/tint/transform/array_length_from_uniform.cc
index 3938b0c..70097f2 100644
--- a/src/tint/transform/array_length_from_uniform.cc
+++ b/src/tint/transform/array_length_from_uniform.cc
@@ -31,13 +31,153 @@
 
 namespace tint::transform {
 
+namespace {
+
+bool ShouldRun(const Program* program) {
+    for (auto* fn : program->AST().Functions()) {
+        if (auto* sem_fn = program->Sem().Get(fn)) {
+            for (auto* builtin : sem_fn->DirectlyCalledBuiltins()) {
+                if (builtin->Type() == sem::BuiltinType::kArrayLength) {
+                    return true;
+                }
+            }
+        }
+    }
+    return false;
+}
+
+}  // namespace
+
 ArrayLengthFromUniform::ArrayLengthFromUniform() = default;
 ArrayLengthFromUniform::~ArrayLengthFromUniform() = default;
 
-/// The PIMPL state for this transform
+/// PIMPL state for the transform
 struct ArrayLengthFromUniform::State {
+    /// Constructor
+    /// @param program the source program
+    /// @param in the input transform data
+    /// @param out the output transform data
+    explicit State(const Program* program, const DataMap& in, DataMap& out)
+        : src(program), inputs(in), outputs(out) {}
+
+    /// Runs the transform
+    /// @returns the new program or SkipTransform if the transform is not required
+    ApplyResult Run() {
+        auto* cfg = inputs.Get<Config>();
+        if (cfg == nullptr) {
+            b.Diagnostics().add_error(diag::System::Transform,
+                                      "missing transform data for " +
+                                          std::string(TypeInfo::Of<ArrayLengthFromUniform>().name));
+            return Program(std::move(b));
+        }
+
+        if (!ShouldRun(ctx.src)) {
+            return SkipTransform;
+        }
+
+        const char* kBufferSizeMemberName = "buffer_size";
+
+        // Determine the size of the buffer size array.
+        uint32_t max_buffer_size_index = 0;
+
+        IterateArrayLengthOnStorageVar([&](const ast::CallExpression*, const sem::VariableUser*,
+                                           const sem::GlobalVariable* var) {
+            auto binding = var->BindingPoint();
+            auto idx_itr = cfg->bindpoint_to_size_index.find(binding);
+            if (idx_itr == cfg->bindpoint_to_size_index.end()) {
+                return;
+            }
+            if (idx_itr->second > max_buffer_size_index) {
+                max_buffer_size_index = idx_itr->second;
+            }
+        });
+
+        // Get (or create, on first call) the uniform buffer that will receive the
+        // size of each storage buffer in the module.
+        const ast::Variable* buffer_size_ubo = nullptr;
+        auto get_ubo = [&]() {
+            if (!buffer_size_ubo) {
+                // Emit an array<vec4<u32>, N>, where N is 1/4 number of elements.
+                // We do this because UBOs require an element stride that is 16-byte
+                // aligned.
+                auto* buffer_size_struct = b.Structure(
+                    b.Sym(), utils::Vector{
+                                 b.Member(kBufferSizeMemberName,
+                                          b.ty.array(b.ty.vec4(b.ty.u32()),
+                                                     u32((max_buffer_size_index / 4) + 1))),
+                             });
+                buffer_size_ubo =
+                    b.GlobalVar(b.Sym(), b.ty.Of(buffer_size_struct), ast::AddressSpace::kUniform,
+                                b.Group(AInt(cfg->ubo_binding.group)),
+                                b.Binding(AInt(cfg->ubo_binding.binding)));
+            }
+            return buffer_size_ubo;
+        };
+
+        std::unordered_set<uint32_t> used_size_indices;
+
+        IterateArrayLengthOnStorageVar([&](const ast::CallExpression* call_expr,
+                                           const sem::VariableUser* storage_buffer_sem,
+                                           const sem::GlobalVariable* var) {
+            auto binding = var->BindingPoint();
+            auto idx_itr = cfg->bindpoint_to_size_index.find(binding);
+            if (idx_itr == cfg->bindpoint_to_size_index.end()) {
+                return;
+            }
+
+            uint32_t size_index = idx_itr->second;
+            used_size_indices.insert(size_index);
+
+            // Load the total storage buffer size from the UBO.
+            uint32_t array_index = size_index / 4;
+            auto* vec_expr = b.IndexAccessor(
+                b.MemberAccessor(get_ubo()->symbol, kBufferSizeMemberName), u32(array_index));
+            uint32_t vec_index = size_index % 4;
+            auto* total_storage_buffer_size = b.IndexAccessor(vec_expr, u32(vec_index));
+
+            // Calculate actual array length
+            //                total_storage_buffer_size - array_offset
+            // array_length = ----------------------------------------
+            //                             array_stride
+            const ast::Expression* total_size = total_storage_buffer_size;
+            auto* storage_buffer_type = storage_buffer_sem->Type()->UnwrapRef();
+            const sem::Array* array_type = nullptr;
+            if (auto* str = storage_buffer_type->As<sem::Struct>()) {
+                // The variable is a struct, so subtract the byte offset of the array
+                // member.
+                auto* array_member_sem = str->Members().back();
+                array_type = array_member_sem->Type()->As<sem::Array>();
+                total_size = b.Sub(total_storage_buffer_size, u32(array_member_sem->Offset()));
+            } else if (auto* arr = storage_buffer_type->As<sem::Array>()) {
+                array_type = arr;
+            } else {
+                TINT_ICE(Transform, b.Diagnostics())
+                    << "expected form of arrayLength argument to be &array_var or "
+                       "&struct_var.array_member";
+                return;
+            }
+            auto* array_length = b.Div(total_size, u32(array_type->Stride()));
+
+            ctx.Replace(call_expr, array_length);
+        });
+
+        outputs.Add<Result>(used_size_indices);
+
+        ctx.Clone();
+        return Program(std::move(b));
+    }
+
+  private:
+    /// The source program
+    const Program* const src;
+    /// The transform inputs
+    const DataMap& inputs;
+    /// The transform outputs
+    DataMap& outputs;
+    /// The target program builder
+    ProgramBuilder b;
     /// The clone context
-    CloneContext& ctx;
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
 
     /// Iterate over all arrayLength() builtins that operate on
     /// storage buffer variables.
@@ -48,10 +188,10 @@
     /// sem::GlobalVariable for the storage buffer.
     template <typename F>
     void IterateArrayLengthOnStorageVar(F&& functor) {
-        auto& sem = ctx.src->Sem();
+        auto& sem = src->Sem();
 
         // Find all calls to the arrayLength() builtin.
-        for (auto* node : ctx.src->ASTNodes().Objects()) {
+        for (auto* node : src->ASTNodes().Objects()) {
             auto* call_expr = node->As<ast::CallExpression>();
             if (!call_expr) {
                 continue;
@@ -79,7 +219,7 @@
             //   arrayLength(&array_var)
             auto* param = call_expr->args[0]->As<ast::UnaryOpExpression>();
             if (!param || param->op != ast::UnaryOp::kAddressOf) {
-                TINT_ICE(Transform, ctx.dst->Diagnostics())
+                TINT_ICE(Transform, b.Diagnostics())
                     << "expected form of arrayLength argument to be &array_var or "
                        "&struct_var.array_member";
                 break;
@@ -90,7 +230,7 @@
             }
             auto* storage_buffer_sem = sem.Get<sem::VariableUser>(storage_buffer_expr);
             if (!storage_buffer_sem) {
-                TINT_ICE(Transform, ctx.dst->Diagnostics())
+                TINT_ICE(Transform, b.Diagnostics())
                     << "expected form of arrayLength argument to be &array_var or "
                        "&struct_var.array_member";
                 break;
@@ -99,8 +239,7 @@
             // Get the index to use for the buffer size array.
             auto* var = tint::As<sem::GlobalVariable>(storage_buffer_sem->Variable());
             if (!var) {
-                TINT_ICE(Transform, ctx.dst->Diagnostics())
-                    << "storage buffer is not a global variable";
+                TINT_ICE(Transform, b.Diagnostics()) << "storage buffer is not a global variable";
                 break;
             }
             functor(call_expr, storage_buffer_sem, var);
@@ -108,117 +247,10 @@
     }
 };
 
-bool ArrayLengthFromUniform::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* fn : program->AST().Functions()) {
-        if (auto* sem_fn = program->Sem().Get(fn)) {
-            for (auto* builtin : sem_fn->DirectlyCalledBuiltins()) {
-                if (builtin->Type() == sem::BuiltinType::kArrayLength) {
-                    return true;
-                }
-            }
-        }
-    }
-    return false;
-}
-
-void ArrayLengthFromUniform::Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const {
-    auto* cfg = inputs.Get<Config>();
-    if (cfg == nullptr) {
-        ctx.dst->Diagnostics().add_error(
-            diag::System::Transform, "missing transform data for " + std::string(TypeInfo().name));
-        return;
-    }
-
-    const char* kBufferSizeMemberName = "buffer_size";
-
-    // Determine the size of the buffer size array.
-    uint32_t max_buffer_size_index = 0;
-
-    State{ctx}.IterateArrayLengthOnStorageVar(
-        [&](const ast::CallExpression*, const sem::VariableUser*, const sem::GlobalVariable* var) {
-            auto binding = var->BindingPoint();
-            auto idx_itr = cfg->bindpoint_to_size_index.find(binding);
-            if (idx_itr == cfg->bindpoint_to_size_index.end()) {
-                return;
-            }
-            if (idx_itr->second > max_buffer_size_index) {
-                max_buffer_size_index = idx_itr->second;
-            }
-        });
-
-    // Get (or create, on first call) the uniform buffer that will receive the
-    // size of each storage buffer in the module.
-    const ast::Variable* buffer_size_ubo = nullptr;
-    auto get_ubo = [&]() {
-        if (!buffer_size_ubo) {
-            // Emit an array<vec4<u32>, N>, where N is 1/4 number of elements.
-            // We do this because UBOs require an element stride that is 16-byte
-            // aligned.
-            auto* buffer_size_struct = ctx.dst->Structure(
-                ctx.dst->Sym(),
-                utils::Vector{
-                    ctx.dst->Member(kBufferSizeMemberName,
-                                    ctx.dst->ty.array(ctx.dst->ty.vec4(ctx.dst->ty.u32()),
-                                                      u32((max_buffer_size_index / 4) + 1))),
-                });
-            buffer_size_ubo = ctx.dst->GlobalVar(ctx.dst->Sym(), ctx.dst->ty.Of(buffer_size_struct),
-                                                 ast::AddressSpace::kUniform,
-                                                 ctx.dst->Group(AInt(cfg->ubo_binding.group)),
-                                                 ctx.dst->Binding(AInt(cfg->ubo_binding.binding)));
-        }
-        return buffer_size_ubo;
-    };
-
-    std::unordered_set<uint32_t> used_size_indices;
-
-    State{ctx}.IterateArrayLengthOnStorageVar([&](const ast::CallExpression* call_expr,
-                                                  const sem::VariableUser* storage_buffer_sem,
-                                                  const sem::GlobalVariable* var) {
-        auto binding = var->BindingPoint();
-        auto idx_itr = cfg->bindpoint_to_size_index.find(binding);
-        if (idx_itr == cfg->bindpoint_to_size_index.end()) {
-            return;
-        }
-
-        uint32_t size_index = idx_itr->second;
-        used_size_indices.insert(size_index);
-
-        // Load the total storage buffer size from the UBO.
-        uint32_t array_index = size_index / 4;
-        auto* vec_expr = ctx.dst->IndexAccessor(
-            ctx.dst->MemberAccessor(get_ubo()->symbol, kBufferSizeMemberName), u32(array_index));
-        uint32_t vec_index = size_index % 4;
-        auto* total_storage_buffer_size = ctx.dst->IndexAccessor(vec_expr, u32(vec_index));
-
-        // Calculate actual array length
-        //                total_storage_buffer_size - array_offset
-        // array_length = ----------------------------------------
-        //                             array_stride
-        const ast::Expression* total_size = total_storage_buffer_size;
-        auto* storage_buffer_type = storage_buffer_sem->Type()->UnwrapRef();
-        const sem::Array* array_type = nullptr;
-        if (auto* str = storage_buffer_type->As<sem::Struct>()) {
-            // The variable is a struct, so subtract the byte offset of the array
-            // member.
-            auto* array_member_sem = str->Members().back();
-            array_type = array_member_sem->Type()->As<sem::Array>();
-            total_size = ctx.dst->Sub(total_storage_buffer_size, u32(array_member_sem->Offset()));
-        } else if (auto* arr = storage_buffer_type->As<sem::Array>()) {
-            array_type = arr;
-        } else {
-            TINT_ICE(Transform, ctx.dst->Diagnostics())
-                << "expected form of arrayLength argument to be &array_var or "
-                   "&struct_var.array_member";
-            return;
-        }
-        auto* array_length = ctx.dst->Div(total_size, u32(array_type->Stride()));
-
-        ctx.Replace(call_expr, array_length);
-    });
-
-    ctx.Clone();
-
-    outputs.Add<Result>(used_size_indices);
+Transform::ApplyResult ArrayLengthFromUniform::Apply(const Program* src,
+                                                     const DataMap& inputs,
+                                                     DataMap& outputs) const {
+    return State{src, inputs, outputs}.Run();
 }
 
 ArrayLengthFromUniform::Config::Config(sem::BindingPoint ubo_bp) : ubo_binding(ubo_bp) {}
diff --git a/src/tint/transform/array_length_from_uniform.h b/src/tint/transform/array_length_from_uniform.h
index 8bd6af5..507ea37 100644
--- a/src/tint/transform/array_length_from_uniform.h
+++ b/src/tint/transform/array_length_from_uniform.h
@@ -100,22 +100,12 @@
         std::unordered_set<uint32_t> used_size_indices;
     };
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
   private:
-    /// The PIMPL state for this transform
     struct State;
 };
 
diff --git a/src/tint/transform/array_length_from_uniform_test.cc b/src/tint/transform/array_length_from_uniform_test.cc
index 1058bf1..b5d9e77 100644
--- a/src/tint/transform/array_length_from_uniform_test.cc
+++ b/src/tint/transform/array_length_from_uniform_test.cc
@@ -28,7 +28,13 @@
 TEST_F(ArrayLengthFromUniformTest, ShouldRunEmptyModule) {
     auto* src = R"()";
 
-    EXPECT_FALSE(ShouldRun<ArrayLengthFromUniform>(src));
+    ArrayLengthFromUniform::Config cfg({0, 30u});
+    cfg.bindpoint_to_size_index.emplace(sem::BindingPoint{0, 0}, 0);
+
+    DataMap data;
+    data.Add<ArrayLengthFromUniform::Config>(std::move(cfg));
+
+    EXPECT_FALSE(ShouldRun<ArrayLengthFromUniform>(src, data));
 }
 
 TEST_F(ArrayLengthFromUniformTest, ShouldRunNoArrayLength) {
@@ -45,7 +51,13 @@
 }
 )";
 
-    EXPECT_FALSE(ShouldRun<ArrayLengthFromUniform>(src));
+    ArrayLengthFromUniform::Config cfg({0, 30u});
+    cfg.bindpoint_to_size_index.emplace(sem::BindingPoint{0, 0}, 0);
+
+    DataMap data;
+    data.Add<ArrayLengthFromUniform::Config>(std::move(cfg));
+
+    EXPECT_FALSE(ShouldRun<ArrayLengthFromUniform>(src, data));
 }
 
 TEST_F(ArrayLengthFromUniformTest, ShouldRunWithArrayLength) {
@@ -63,7 +75,13 @@
 }
 )";
 
-    EXPECT_TRUE(ShouldRun<ArrayLengthFromUniform>(src));
+    ArrayLengthFromUniform::Config cfg({0, 30u});
+    cfg.bindpoint_to_size_index.emplace(sem::BindingPoint{0, 0}, 0);
+
+    DataMap data;
+    data.Add<ArrayLengthFromUniform::Config>(std::move(cfg));
+
+    EXPECT_TRUE(ShouldRun<ArrayLengthFromUniform>(src, data));
 }
 
 TEST_F(ArrayLengthFromUniformTest, Error_MissingTransformData) {
diff --git a/src/tint/transform/binding_remapper.cc b/src/tint/transform/binding_remapper.cc
index 798b228..0781355 100644
--- a/src/tint/transform/binding_remapper.cc
+++ b/src/tint/transform/binding_remapper.cc
@@ -40,19 +40,21 @@
 BindingRemapper::BindingRemapper() = default;
 BindingRemapper::~BindingRemapper() = default;
 
-bool BindingRemapper::ShouldRun(const Program*, const DataMap& inputs) const {
-    if (auto* remappings = inputs.Get<Remappings>()) {
-        return !remappings->binding_points.empty() || !remappings->access_controls.empty();
-    }
-    return false;
-}
+Transform::ApplyResult BindingRemapper::Apply(const Program* src,
+                                              const DataMap& inputs,
+                                              DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
 
-void BindingRemapper::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) const {
     auto* remappings = inputs.Get<Remappings>();
     if (!remappings) {
-        ctx.dst->Diagnostics().add_error(
-            diag::System::Transform, "missing transform data for " + std::string(TypeInfo().name));
-        return;
+        b.Diagnostics().add_error(diag::System::Transform,
+                                  "missing transform data for " + std::string(TypeInfo().name));
+        return Program(std::move(b));
+    }
+
+    if (remappings->binding_points.empty() && remappings->access_controls.empty()) {
+        return SkipTransform;
     }
 
     // A set of post-remapped binding points that need to be decorated with a
@@ -62,11 +64,11 @@
     if (remappings->allow_collisions) {
         // Scan for binding point collisions generated by this transform.
         // Populate all collisions in the `add_collision_attr` set.
-        for (auto* func_ast : ctx.src->AST().Functions()) {
+        for (auto* func_ast : src->AST().Functions()) {
             if (!func_ast->IsEntryPoint()) {
                 continue;
             }
-            auto* func = ctx.src->Sem().Get(func_ast);
+            auto* func = src->Sem().Get(func_ast);
             std::unordered_map<sem::BindingPoint, int> binding_point_counts;
             for (auto* global : func->TransitivelyReferencedGlobals()) {
                 if (global->Declaration()->HasBindingPoint()) {
@@ -90,9 +92,9 @@
         }
     }
 
-    for (auto* var : ctx.src->AST().Globals<ast::Var>()) {
+    for (auto* var : src->AST().Globals<ast::Var>()) {
         if (var->HasBindingPoint()) {
-            auto* global_sem = ctx.src->Sem().Get<sem::GlobalVariable>(var);
+            auto* global_sem = src->Sem().Get<sem::GlobalVariable>(var);
 
             // The original binding point
             BindingPoint from = global_sem->BindingPoint();
@@ -106,8 +108,8 @@
             auto bp_it = remappings->binding_points.find(from);
             if (bp_it != remappings->binding_points.end()) {
                 BindingPoint to = bp_it->second;
-                auto* new_group = ctx.dst->Group(AInt(to.group));
-                auto* new_binding = ctx.dst->Binding(AInt(to.binding));
+                auto* new_group = b.Group(AInt(to.group));
+                auto* new_binding = b.Binding(AInt(to.binding));
 
                 auto* old_group = ast::GetAttribute<ast::GroupAttribute>(var->attributes);
                 auto* old_binding = ast::GetAttribute<ast::BindingAttribute>(var->attributes);
@@ -122,37 +124,37 @@
             if (ac_it != remappings->access_controls.end()) {
                 ast::Access ac = ac_it->second;
                 if (ac == ast::Access::kUndefined) {
-                    ctx.dst->Diagnostics().add_error(
+                    b.Diagnostics().add_error(
                         diag::System::Transform,
                         "invalid access mode (" + std::to_string(static_cast<uint32_t>(ac)) + ")");
-                    return;
+                    return Program(std::move(b));
                 }
-                auto* sem = ctx.src->Sem().Get(var);
+                auto* sem = src->Sem().Get(var);
                 if (sem->AddressSpace() != ast::AddressSpace::kStorage) {
-                    ctx.dst->Diagnostics().add_error(
+                    b.Diagnostics().add_error(
                         diag::System::Transform,
                         "cannot apply access control to variable with address space " +
                             std::string(utils::ToString(sem->AddressSpace())));
-                    return;
+                    return Program(std::move(b));
                 }
                 auto* ty = sem->Type()->UnwrapRef();
                 const ast::Type* inner_ty = CreateASTTypeFor(ctx, ty);
-                auto* new_var =
-                    ctx.dst->Var(ctx.Clone(var->source), ctx.Clone(var->symbol), inner_ty,
-                                 var->declared_address_space, ac, ctx.Clone(var->initializer),
-                                 ctx.Clone(var->attributes));
+                auto* new_var = b.Var(ctx.Clone(var->source), ctx.Clone(var->symbol), inner_ty,
+                                      var->declared_address_space, ac, ctx.Clone(var->initializer),
+                                      ctx.Clone(var->attributes));
                 ctx.Replace(var, new_var);
             }
 
             // Add `DisableValidationAttribute`s if required
             if (add_collision_attr.count(bp)) {
-                auto* attribute = ctx.dst->Disable(ast::DisabledValidation::kBindingPointCollision);
+                auto* attribute = b.Disable(ast::DisabledValidation::kBindingPointCollision);
                 ctx.InsertBefore(var->attributes, *var->attributes.begin(), attribute);
             }
         }
     }
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/binding_remapper.h b/src/tint/transform/binding_remapper.h
index 77fc5bc..b0efe0d 100644
--- a/src/tint/transform/binding_remapper.h
+++ b/src/tint/transform/binding_remapper.h
@@ -67,19 +67,10 @@
     BindingRemapper();
     ~BindingRemapper() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/binding_remapper_test.cc b/src/tint/transform/binding_remapper_test.cc
index 564a3a5..5bafb7e 100644
--- a/src/tint/transform/binding_remapper_test.cc
+++ b/src/tint/transform/binding_remapper_test.cc
@@ -23,12 +23,6 @@
 
 using BindingRemapperTest = TransformTest;
 
-TEST_F(BindingRemapperTest, ShouldRunNoRemappings) {
-    auto* src = R"()";
-
-    EXPECT_FALSE(ShouldRun<BindingRemapper>(src));
-}
-
 TEST_F(BindingRemapperTest, ShouldRunEmptyRemappings) {
     auto* src = R"()";
 
@@ -350,7 +344,7 @@
 }
 )";
 
-    auto* expect = src;
+    auto* expect = R"(error: missing transform data for tint::transform::BindingRemapper)";
 
     auto got = Run<BindingRemapper>(src);
 
diff --git a/src/tint/transform/builtin_polyfill.cc b/src/tint/transform/builtin_polyfill.cc
index 1e28e7e..db200e4 100644
--- a/src/tint/transform/builtin_polyfill.cc
+++ b/src/tint/transform/builtin_polyfill.cc
@@ -29,7 +29,7 @@
 
 namespace tint::transform {
 
-/// The PIMPL state for the BuiltinPolyfill transform
+/// PIMPL state for the transform
 struct BuiltinPolyfill::State {
     /// Constructor
     /// @param c the CloneContext
@@ -604,193 +604,100 @@
 
 BuiltinPolyfill::~BuiltinPolyfill() = default;
 
-bool BuiltinPolyfill::ShouldRun(const Program* program, const DataMap& data) const {
-    if (auto* cfg = data.Get<Config>()) {
-        auto builtins = cfg->builtins;
-        auto& sem = program->Sem();
-        for (auto* node : program->ASTNodes().Objects()) {
-            if (auto* call = sem.Get<sem::Call>(node)) {
-                if (auto* builtin = call->Target()->As<sem::Builtin>()) {
-                    if (call->Stage() == sem::EvaluationStage::kConstant) {
-                        continue;  // Don't polyfill @const expressions
-                    }
-                    switch (builtin->Type()) {
-                        case sem::BuiltinType::kAcosh:
-                            if (builtins.acosh != Level::kNone) {
-                                return true;
-                            }
-                            break;
-                        case sem::BuiltinType::kAsinh:
-                            if (builtins.asinh) {
-                                return true;
-                            }
-                            break;
-                        case sem::BuiltinType::kAtanh:
-                            if (builtins.atanh != Level::kNone) {
-                                return true;
-                            }
-                            break;
-                        case sem::BuiltinType::kClamp:
-                            if (builtins.clamp_int) {
-                                auto& sig = builtin->Signature();
-                                return sig.parameters[0]->Type()->is_integer_scalar_or_vector();
-                            }
-                            break;
-                        case sem::BuiltinType::kCountLeadingZeros:
-                            if (builtins.count_leading_zeros) {
-                                return true;
-                            }
-                            break;
-                        case sem::BuiltinType::kCountTrailingZeros:
-                            if (builtins.count_trailing_zeros) {
-                                return true;
-                            }
-                            break;
-                        case sem::BuiltinType::kExtractBits:
-                            if (builtins.extract_bits != Level::kNone) {
-                                return true;
-                            }
-                            break;
-                        case sem::BuiltinType::kFirstLeadingBit:
-                            if (builtins.first_leading_bit) {
-                                return true;
-                            }
-                            break;
-                        case sem::BuiltinType::kFirstTrailingBit:
-                            if (builtins.first_trailing_bit) {
-                                return true;
-                            }
-                            break;
-                        case sem::BuiltinType::kInsertBits:
-                            if (builtins.insert_bits != Level::kNone) {
-                                return true;
-                            }
-                            break;
-                        case sem::BuiltinType::kSaturate:
-                            if (builtins.saturate) {
-                                return true;
-                            }
-                            break;
-                        case sem::BuiltinType::kTextureSampleBaseClampToEdge:
-                            if (builtins.texture_sample_base_clamp_to_edge_2d_f32) {
-                                auto& sig = builtin->Signature();
-                                auto* tex = sig.Parameter(sem::ParameterUsage::kTexture);
-                                if (auto* stex = tex->Type()->As<sem::SampledTexture>()) {
-                                    return stex->type()->Is<sem::F32>();
-                                }
-                            }
-                            break;
-                        case sem::BuiltinType::kQuantizeToF16:
-                            if (builtins.quantize_to_vec_f16) {
-                                if (builtin->ReturnType()->Is<sem::Vector>()) {
-                                    return true;
-                                }
-                            }
-                            break;
-                        default:
-                            break;
-                    }
-                }
-            }
-        }
-    }
-    return false;
-}
-
-void BuiltinPolyfill::Run(CloneContext& ctx, const DataMap& data, DataMap&) const {
+Transform::ApplyResult BuiltinPolyfill::Apply(const Program* src,
+                                              const DataMap& data,
+                                              DataMap&) const {
     auto* cfg = data.Get<Config>();
     if (!cfg) {
-        ctx.Clone();
-        return;
+        return SkipTransform;
     }
 
-    std::unordered_map<const sem::Builtin*, Symbol> polyfills;
+    auto& builtins = cfg->builtins;
 
-    ctx.ReplaceAll([&](const ast::CallExpression* expr) -> const ast::CallExpression* {
-        auto builtins = cfg->builtins;
-        State s{ctx, builtins};
-        if (auto* call = s.sem.Get<sem::Call>(expr)) {
+    utils::Hashmap<const sem::Builtin*, Symbol, 8> polyfills;
+
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+    State s{ctx, builtins};
+
+    bool made_changes = false;
+    for (auto* node : src->ASTNodes().Objects()) {
+        if (auto* call = src->Sem().Get<sem::Call>(node)) {
             if (auto* builtin = call->Target()->As<sem::Builtin>()) {
                 if (call->Stage() == sem::EvaluationStage::kConstant) {
-                    return nullptr;  // Don't polyfill @const expressions
+                    continue;  // Don't polyfill @const expressions
                 }
                 Symbol polyfill;
                 switch (builtin->Type()) {
                     case sem::BuiltinType::kAcosh:
                         if (builtins.acosh != Level::kNone) {
-                            polyfill = utils::GetOrCreate(
-                                polyfills, builtin, [&] { return s.acosh(builtin->ReturnType()); });
+                            polyfill = polyfills.GetOrCreate(
+                                builtin, [&] { return s.acosh(builtin->ReturnType()); });
                         }
                         break;
                     case sem::BuiltinType::kAsinh:
                         if (builtins.asinh) {
-                            polyfill = utils::GetOrCreate(
-                                polyfills, builtin, [&] { return s.asinh(builtin->ReturnType()); });
+                            polyfill = polyfills.GetOrCreate(
+                                builtin, [&] { return s.asinh(builtin->ReturnType()); });
                         }
                         break;
                     case sem::BuiltinType::kAtanh:
                         if (builtins.atanh != Level::kNone) {
-                            polyfill = utils::GetOrCreate(
-                                polyfills, builtin, [&] { return s.atanh(builtin->ReturnType()); });
+                            polyfill = polyfills.GetOrCreate(
+                                builtin, [&] { return s.atanh(builtin->ReturnType()); });
                         }
                         break;
                     case sem::BuiltinType::kClamp:
                         if (builtins.clamp_int) {
                             auto& sig = builtin->Signature();
                             if (sig.parameters[0]->Type()->is_integer_scalar_or_vector()) {
-                                polyfill = utils::GetOrCreate(polyfills, builtin, [&] {
-                                    return s.clampInteger(builtin->ReturnType());
-                                });
+                                polyfill = polyfills.GetOrCreate(
+                                    builtin, [&] { return s.clampInteger(builtin->ReturnType()); });
                             }
                         }
                         break;
                     case sem::BuiltinType::kCountLeadingZeros:
                         if (builtins.count_leading_zeros) {
-                            polyfill = utils::GetOrCreate(polyfills, builtin, [&] {
+                            polyfill = polyfills.GetOrCreate(builtin, [&] {
                                 return s.countLeadingZeros(builtin->ReturnType());
                             });
                         }
                         break;
                     case sem::BuiltinType::kCountTrailingZeros:
                         if (builtins.count_trailing_zeros) {
-                            polyfill = utils::GetOrCreate(polyfills, builtin, [&] {
+                            polyfill = polyfills.GetOrCreate(builtin, [&] {
                                 return s.countTrailingZeros(builtin->ReturnType());
                             });
                         }
                         break;
                     case sem::BuiltinType::kExtractBits:
                         if (builtins.extract_bits != Level::kNone) {
-                            polyfill = utils::GetOrCreate(polyfills, builtin, [&] {
-                                return s.extractBits(builtin->ReturnType());
-                            });
+                            polyfill = polyfills.GetOrCreate(
+                                builtin, [&] { return s.extractBits(builtin->ReturnType()); });
                         }
                         break;
                     case sem::BuiltinType::kFirstLeadingBit:
                         if (builtins.first_leading_bit) {
-                            polyfill = utils::GetOrCreate(polyfills, builtin, [&] {
-                                return s.firstLeadingBit(builtin->ReturnType());
-                            });
+                            polyfill = polyfills.GetOrCreate(
+                                builtin, [&] { return s.firstLeadingBit(builtin->ReturnType()); });
                         }
                         break;
                     case sem::BuiltinType::kFirstTrailingBit:
                         if (builtins.first_trailing_bit) {
-                            polyfill = utils::GetOrCreate(polyfills, builtin, [&] {
-                                return s.firstTrailingBit(builtin->ReturnType());
-                            });
+                            polyfill = polyfills.GetOrCreate(
+                                builtin, [&] { return s.firstTrailingBit(builtin->ReturnType()); });
                         }
                         break;
                     case sem::BuiltinType::kInsertBits:
                         if (builtins.insert_bits != Level::kNone) {
-                            polyfill = utils::GetOrCreate(polyfills, builtin, [&] {
-                                return s.insertBits(builtin->ReturnType());
-                            });
+                            polyfill = polyfills.GetOrCreate(
+                                builtin, [&] { return s.insertBits(builtin->ReturnType()); });
                         }
                         break;
                     case sem::BuiltinType::kSaturate:
                         if (builtins.saturate) {
-                            polyfill = utils::GetOrCreate(polyfills, builtin, [&] {
-                                return s.saturate(builtin->ReturnType());
-                            });
+                            polyfill = polyfills.GetOrCreate(
+                                builtin, [&] { return s.saturate(builtin->ReturnType()); });
                         }
                         break;
                     case sem::BuiltinType::kTextureSampleBaseClampToEdge:
@@ -799,7 +706,7 @@
                             auto* tex = sig.Parameter(sem::ParameterUsage::kTexture);
                             if (auto* stex = tex->Type()->As<sem::SampledTexture>()) {
                                 if (stex->type()->Is<sem::F32>()) {
-                                    polyfill = utils::GetOrCreate(polyfills, builtin, [&] {
+                                    polyfill = polyfills.GetOrCreate(builtin, [&] {
                                         return s.textureSampleBaseClampToEdge_2d_f32();
                                     });
                                 }
@@ -809,8 +716,8 @@
                     case sem::BuiltinType::kQuantizeToF16:
                         if (builtins.quantize_to_vec_f16) {
                             if (auto* vec = builtin->ReturnType()->As<sem::Vector>()) {
-                                polyfill = utils::GetOrCreate(polyfills, builtin,
-                                                              [&] { return s.quantizeToF16(vec); });
+                                polyfill = polyfills.GetOrCreate(
+                                    builtin, [&] { return s.quantizeToF16(vec); });
                             }
                         }
                         break;
@@ -819,14 +726,20 @@
                         break;
                 }
                 if (polyfill.IsValid()) {
-                    return s.b.Call(polyfill, ctx.Clone(call->Declaration()->args));
+                    auto* replacement = s.b.Call(polyfill, ctx.Clone(call->Declaration()->args));
+                    ctx.Replace(call->Declaration(), replacement);
+                    made_changes = true;
                 }
             }
         }
-        return nullptr;
-    });
+    }
+
+    if (!made_changes) {
+        return SkipTransform;
+    }
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 BuiltinPolyfill::Config::Config(const Builtins& b) : builtins(b) {}
diff --git a/src/tint/transform/builtin_polyfill.h b/src/tint/transform/builtin_polyfill.h
index 7106915..231d753 100644
--- a/src/tint/transform/builtin_polyfill.h
+++ b/src/tint/transform/builtin_polyfill.h
@@ -87,21 +87,13 @@
         const Builtins builtins;
     };
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-  protected:
+  private:
     struct State;
-
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/builtin_polyfill_test.cc b/src/tint/transform/builtin_polyfill_test.cc
index 65547ab..4bff0ff 100644
--- a/src/tint/transform/builtin_polyfill_test.cc
+++ b/src/tint/transform/builtin_polyfill_test.cc
@@ -1561,7 +1561,8 @@
 TEST_F(BuiltinPolyfillTest, DISABLED_InsertBits_ConstantExpression) {
     auto* src = R"(
 fn f() {
-  let r : i32 = insertBits(1234, 5678, 5u, 6u);
+  let v = 1234i;
+  let r : i32 = insertBits(v, 5678, 5u, 6u);
 }
 )";
 
@@ -1975,10 +1976,6 @@
 )";
 
     auto* expect = R"(
-@group(0) @binding(0) var t : texture_2d<f32>;
-
-@group(0) @binding(1) var s : sampler;
-
 fn tint_textureSampleBaseClampToEdge(t : texture_2d<f32>, s : sampler, coord : vec2<f32>) -> vec4<f32> {
   let dims = vec2<f32>(textureDimensions(t, 0));
   let half_texel = (vec2<f32>(0.5) / dims);
@@ -1986,6 +1983,10 @@
   return textureSampleLevel(t, s, clamped, 0);
 }
 
+@group(0) @binding(0) var t : texture_2d<f32>;
+
+@group(0) @binding(1) var s : sampler;
+
 fn f() {
   let r = tint_textureSampleBaseClampToEdge(t, s, vec2<f32>(0.5));
 }
diff --git a/src/tint/transform/calculate_array_length.cc b/src/tint/transform/calculate_array_length.cc
index 2ca5e54..9dcdd7b 100644
--- a/src/tint/transform/calculate_array_length.cc
+++ b/src/tint/transform/calculate_array_length.cc
@@ -40,6 +40,19 @@
 
 namespace {
 
+bool ShouldRun(const Program* program) {
+    for (auto* fn : program->AST().Functions()) {
+        if (auto* sem_fn = program->Sem().Get(fn)) {
+            for (auto* builtin : sem_fn->DirectlyCalledBuiltins()) {
+                if (builtin->Type() == sem::BuiltinType::kArrayLength) {
+                    return true;
+                }
+            }
+        }
+    }
+    return false;
+}
+
 /// ArrayUsage describes a runtime array usage.
 /// It is used as a key by the array_length_by_usage map.
 struct ArrayUsage {
@@ -73,21 +86,16 @@
 CalculateArrayLength::CalculateArrayLength() = default;
 CalculateArrayLength::~CalculateArrayLength() = default;
 
-bool CalculateArrayLength::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* fn : program->AST().Functions()) {
-        if (auto* sem_fn = program->Sem().Get(fn)) {
-            for (auto* builtin : sem_fn->DirectlyCalledBuiltins()) {
-                if (builtin->Type() == sem::BuiltinType::kArrayLength) {
-                    return true;
-                }
-            }
-        }
+Transform::ApplyResult CalculateArrayLength::Apply(const Program* src,
+                                                   const DataMap&,
+                                                   DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
     }
-    return false;
-}
 
-void CalculateArrayLength::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    auto& sem = ctx.src->Sem();
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+    auto& sem = src->Sem();
 
     // get_buffer_size_intrinsic() emits the function decorated with
     // BufferSizeIntrinsic that is transformed by the HLSL writer into a call to
@@ -95,24 +103,20 @@
     std::unordered_map<const sem::Reference*, Symbol> buffer_size_intrinsics;
     auto get_buffer_size_intrinsic = [&](const sem::Reference* buffer_type) {
         return utils::GetOrCreate(buffer_size_intrinsics, buffer_type, [&] {
-            auto name = ctx.dst->Sym();
+            auto name = b.Sym();
             auto* type = CreateASTTypeFor(ctx, buffer_type);
-            auto* disable_validation =
-                ctx.dst->Disable(ast::DisabledValidation::kFunctionParameter);
-            ctx.dst->AST().AddFunction(ctx.dst->create<ast::Function>(
+            auto* disable_validation = b.Disable(ast::DisabledValidation::kFunctionParameter);
+            b.AST().AddFunction(b.create<ast::Function>(
                 name,
                 utils::Vector{
-                    ctx.dst->Param("buffer",
-                                   ctx.dst->ty.pointer(type, buffer_type->AddressSpace(),
-                                                       buffer_type->Access()),
-                                   utils::Vector{disable_validation}),
-                    ctx.dst->Param("result", ctx.dst->ty.pointer(ctx.dst->ty.u32(),
-                                                                 ast::AddressSpace::kFunction)),
+                    b.Param("buffer",
+                            b.ty.pointer(type, buffer_type->AddressSpace(), buffer_type->Access()),
+                            utils::Vector{disable_validation}),
+                    b.Param("result", b.ty.pointer(b.ty.u32(), ast::AddressSpace::kFunction)),
                 },
-                ctx.dst->ty.void_(), nullptr,
+                b.ty.void_(), nullptr,
                 utils::Vector{
-                    ctx.dst->ASTNodes().Create<BufferSizeIntrinsic>(ctx.dst->ID(),
-                                                                    ctx.dst->AllocateNodeID()),
+                    b.ASTNodes().Create<BufferSizeIntrinsic>(b.ID(), b.AllocateNodeID()),
                 },
                 utils::Empty));
 
@@ -123,7 +127,7 @@
     std::unordered_map<ArrayUsage, Symbol, ArrayUsage::Hasher> array_length_by_usage;
 
     // Find all the arrayLength() calls...
-    for (auto* node : ctx.src->ASTNodes().Objects()) {
+    for (auto* node : src->ASTNodes().Objects()) {
         if (auto* call_expr = node->As<ast::CallExpression>()) {
             auto* call = sem.Get(call_expr)->UnwrapMaterialize()->As<sem::Call>();
             if (auto* builtin = call->Target()->As<sem::Builtin>()) {
@@ -149,7 +153,7 @@
                     auto* arg = call_expr->args[0];
                     auto* address_of = arg->As<ast::UnaryOpExpression>();
                     if (!address_of || address_of->op != ast::UnaryOp::kAddressOf) {
-                        TINT_ICE(Transform, ctx.dst->Diagnostics())
+                        TINT_ICE(Transform, b.Diagnostics())
                             << "arrayLength() expected address-of, got " << arg->TypeInfo().name;
                     }
                     auto* storage_buffer_expr = address_of->expr;
@@ -158,7 +162,7 @@
                     }
                     auto* storage_buffer_sem = sem.Get<sem::VariableUser>(storage_buffer_expr);
                     if (!storage_buffer_sem) {
-                        TINT_ICE(Transform, ctx.dst->Diagnostics())
+                        TINT_ICE(Transform, b.Diagnostics())
                             << "expected form of arrayLength argument to be &array_var or "
                                "&struct_var.array_member";
                         break;
@@ -179,25 +183,24 @@
 
                             // Construct the variable that'll hold the result of
                             // RWByteAddressBuffer.GetDimensions()
-                            auto* buffer_size_result = ctx.dst->Decl(ctx.dst->Var(
-                                ctx.dst->Sym(), ctx.dst->ty.u32(), ctx.dst->Expr(0_u)));
+                            auto* buffer_size_result =
+                                b.Decl(b.Var(b.Sym(), b.ty.u32(), b.Expr(0_u)));
 
                             // Call storage_buffer.GetDimensions(&buffer_size_result)
-                            auto* call_get_dims = ctx.dst->CallStmt(ctx.dst->Call(
+                            auto* call_get_dims = b.CallStmt(b.Call(
                                 // BufferSizeIntrinsic(X, ARGS...) is
                                 // translated to:
                                 //  X.GetDimensions(ARGS..) by the writer
-                                buffer_size, ctx.dst->AddressOf(ctx.Clone(storage_buffer_expr)),
-                                ctx.dst->AddressOf(
-                                    ctx.dst->Expr(buffer_size_result->variable->symbol))));
+                                buffer_size, b.AddressOf(ctx.Clone(storage_buffer_expr)),
+                                b.AddressOf(b.Expr(buffer_size_result->variable->symbol))));
 
                             // Calculate actual array length
                             //                total_storage_buffer_size - array_offset
                             // array_length = ----------------------------------------
                             //                             array_stride
-                            auto name = ctx.dst->Sym();
+                            auto name = b.Sym();
                             const ast::Expression* total_size =
-                                ctx.dst->Expr(buffer_size_result->variable);
+                                b.Expr(buffer_size_result->variable);
 
                             const sem::Array* array_type = Switch(
                                 storage_buffer_type->StoreType(),
@@ -205,23 +208,21 @@
                                     // The variable is a struct, so subtract the byte offset of
                                     // the array member.
                                     auto* array_member_sem = str->Members().back();
-                                    total_size =
-                                        ctx.dst->Sub(total_size, u32(array_member_sem->Offset()));
+                                    total_size = b.Sub(total_size, u32(array_member_sem->Offset()));
                                     return array_member_sem->Type()->As<sem::Array>();
                                 },
                                 [&](const sem::Array* arr) { return arr; });
 
                             if (!array_type) {
-                                TINT_ICE(Transform, ctx.dst->Diagnostics())
+                                TINT_ICE(Transform, b.Diagnostics())
                                     << "expected form of arrayLength argument to be "
                                        "&array_var or &struct_var.array_member";
                                 return name;
                             }
 
                             uint32_t array_stride = array_type->Size();
-                            auto* array_length_var = ctx.dst->Decl(
-                                ctx.dst->Let(name, ctx.dst->ty.u32(),
-                                             ctx.dst->Div(total_size, u32(array_stride))));
+                            auto* array_length_var = b.Decl(
+                                b.Let(name, b.ty.u32(), b.Div(total_size, u32(array_stride))));
 
                             // Insert the array length calculations at the top of the block
                             ctx.InsertBefore(block->statements, block->statements[0],
@@ -234,13 +235,14 @@
                         });
 
                     // Replace the call to arrayLength() with the array length variable
-                    ctx.Replace(call_expr, ctx.dst->Expr(array_length));
+                    ctx.Replace(call_expr, b.Expr(array_length));
                 }
             }
         }
     }
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/calculate_array_length.h b/src/tint/transform/calculate_array_length.h
index 8db8dcc..e5714a8 100644
--- a/src/tint/transform/calculate_array_length.h
+++ b/src/tint/transform/calculate_array_length.h
@@ -59,19 +59,10 @@
     /// Destructor
     ~CalculateArrayLength() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/canonicalize_entry_point_io.cc b/src/tint/transform/canonicalize_entry_point_io.cc
index b990965..8a14fb7 100644
--- a/src/tint/transform/canonicalize_entry_point_io.cc
+++ b/src/tint/transform/canonicalize_entry_point_io.cc
@@ -123,7 +123,7 @@
 
 }  // namespace
 
-/// State holds the current transform state for a single entry point.
+/// PIMPL state for the transform
 struct CanonicalizeEntryPointIO::State {
     /// OutputValue represents a shader result that the wrapper function produces.
     struct OutputValue {
@@ -770,17 +770,22 @@
     }
 };
 
-void CanonicalizeEntryPointIO::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) const {
+Transform::ApplyResult CanonicalizeEntryPointIO::Apply(const Program* src,
+                                                       const DataMap& inputs,
+                                                       DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     auto* cfg = inputs.Get<Config>();
     if (cfg == nullptr) {
-        ctx.dst->Diagnostics().add_error(
-            diag::System::Transform, "missing transform data for " + std::string(TypeInfo().name));
-        return;
+        b.Diagnostics().add_error(diag::System::Transform,
+                                  "missing transform data for " + std::string(TypeInfo().name));
+        return Program(std::move(b));
     }
 
     // Remove entry point IO attributes from struct declarations.
     // New structures will be created for each entry point, as necessary.
-    for (auto* ty : ctx.src->AST().TypeDecls()) {
+    for (auto* ty : src->AST().TypeDecls()) {
         if (auto* struct_ty = ty->As<ast::Struct>()) {
             for (auto* member : struct_ty->members) {
                 for (auto* attr : member->attributes) {
@@ -792,7 +797,7 @@
         }
     }
 
-    for (auto* func_ast : ctx.src->AST().Functions()) {
+    for (auto* func_ast : src->AST().Functions()) {
         if (!func_ast->IsEntryPoint()) {
             continue;
         }
@@ -802,6 +807,7 @@
     }
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 CanonicalizeEntryPointIO::Config::Config(ShaderStyle style,
diff --git a/src/tint/transform/canonicalize_entry_point_io.h b/src/tint/transform/canonicalize_entry_point_io.h
index 95f8b19..fbfed5e 100644
--- a/src/tint/transform/canonicalize_entry_point_io.h
+++ b/src/tint/transform/canonicalize_entry_point_io.h
@@ -127,15 +127,12 @@
     CanonicalizeEntryPointIO();
     ~CanonicalizeEntryPointIO() override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
+  private:
     struct State;
 };
 
diff --git a/src/tint/transform/clamp_frag_depth.cc b/src/tint/transform/clamp_frag_depth.cc
index e67dda3..4551925 100644
--- a/src/tint/transform/clamp_frag_depth.cc
+++ b/src/tint/transform/clamp_frag_depth.cc
@@ -14,7 +14,7 @@
 
 #include "src/tint/transform/clamp_frag_depth.h"
 
- #include <utility>
+#include <utility>
 
 #include "src/tint/ast/attribute.h"
 #include "src/tint/ast/builtin_attribute.h"
@@ -64,12 +64,7 @@
     return false;
 }
 
-}  // anonymous namespace
-
-ClampFragDepth::ClampFragDepth() = default;
-ClampFragDepth::~ClampFragDepth() = default;
-
-bool ClampFragDepth::ShouldRun(const Program* program, const DataMap&) const {
+bool ShouldRun(const Program* program) {
     auto& sem = program->Sem();
 
     for (auto* fn : program->AST().Functions()) {
@@ -82,22 +77,33 @@
     return false;
 }
 
-void ClampFragDepth::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+}  // anonymous namespace
+
+ClampFragDepth::ClampFragDepth() = default;
+ClampFragDepth::~ClampFragDepth() = default;
+
+Transform::ApplyResult ClampFragDepth::Apply(const Program* src, const DataMap&, DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     // Abort on any use of push constants in the module.
-    for (auto* global : ctx.src->AST().GlobalVariables()) {
+    for (auto* global : src->AST().GlobalVariables()) {
         if (auto* var = global->As<ast::Var>()) {
             if (var->declared_address_space == ast::AddressSpace::kPushConstant) {
-                TINT_ICE(Transform, ctx.dst->Diagnostics())
+                TINT_ICE(Transform, b.Diagnostics())
                     << "ClampFragDepth doesn't know how to handle module that already use push "
                        "constants.";
-                return;
+                return Program(std::move(b));
             }
         }
     }
 
-    auto& b = *ctx.dst;
-    auto& sem = ctx.src->Sem();
-    auto& sym = ctx.src->Symbols();
+    if (!ShouldRun(src)) {
+        return SkipTransform;
+    }
+
+    auto& sem = src->Sem();
+    auto& sym = src->Symbols();
 
     // At least one entry-point needs clamping. Add the following to the module:
     //
@@ -197,6 +203,7 @@
     });
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/clamp_frag_depth.h b/src/tint/transform/clamp_frag_depth.h
index 3b15f11..1e9d0d6 100644
--- a/src/tint/transform/clamp_frag_depth.h
+++ b/src/tint/transform/clamp_frag_depth.h
@@ -61,19 +61,10 @@
     /// Destructor
     ~ClampFragDepth() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/combine_samplers.cc b/src/tint/transform/combine_samplers.cc
index 97650ad..e7286d4 100644
--- a/src/tint/transform/combine_samplers.cc
+++ b/src/tint/transform/combine_samplers.cc
@@ -47,10 +47,14 @@
 CombineSamplers::BindingInfo::BindingInfo(const BindingInfo& other) = default;
 CombineSamplers::BindingInfo::~BindingInfo() = default;
 
-/// The PIMPL state for the CombineSamplers transform
+/// PIMPL state for the transform
 struct CombineSamplers::State {
+    /// The source program
+    const Program* const src;
+    /// The target program builder
+    ProgramBuilder b;
     /// The clone context
-    CloneContext& ctx;
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
 
     /// The binding info
     const BindingInfo* binding_info;
@@ -88,9 +92,9 @@
     }
 
     /// Constructor
-    /// @param context the clone context
+    /// @param program the source program
     /// @param info the binding map information
-    State(CloneContext& context, const BindingInfo* info) : ctx(context), binding_info(info) {}
+    State(const Program* program, const BindingInfo* info) : src(program), binding_info(info) {}
 
     /// Creates a combined sampler global variables.
     /// (Note this is actually a Texture node at the AST level, but it will be
@@ -145,8 +149,9 @@
         }
     }
 
-    /// Performs the transformation
-    void Run() {
+    /// Runs the transform
+    /// @returns the new program or SkipTransform if the transform is not required
+    ApplyResult Run() {
         auto& sem = ctx.src->Sem();
 
         // Remove all texture and sampler global variables. These will be replaced
@@ -169,14 +174,14 @@
 
         // Rewrite all function signatures to use combined samplers, and remove
         // separate textures & samplers. Create new combined globals where found.
-        ctx.ReplaceAll([&](const ast::Function* src) -> const ast::Function* {
-            if (auto* func = sem.Get(src)) {
-                auto pairs = func->TextureSamplerPairs();
+        ctx.ReplaceAll([&](const ast::Function* ast_fn) -> const ast::Function* {
+            if (auto* fn = sem.Get(ast_fn)) {
+                auto pairs = fn->TextureSamplerPairs();
                 if (pairs.IsEmpty()) {
                     return nullptr;
                 }
                 utils::Vector<const ast::Parameter*, 8> params;
-                for (auto pair : func->TextureSamplerPairs()) {
+                for (auto pair : fn->TextureSamplerPairs()) {
                     const sem::Variable* texture_var = pair.first;
                     const sem::Variable* sampler_var = pair.second;
                     std::string name =
@@ -197,23 +202,23 @@
                         auto* type = CreateCombinedASTTypeFor(texture_var, sampler_var);
                         auto* var = ctx.dst->Param(ctx.dst->Symbols().New(name), type);
                         params.Push(var);
-                        function_combined_texture_samplers_[func][pair] = var;
+                        function_combined_texture_samplers_[fn][pair] = var;
                     }
                 }
                 // Filter out separate textures and samplers from the original
                 // function signature.
-                for (auto* var : src->params) {
-                    if (!sem.Get(var->type)->IsAnyOf<sem::Texture, sem::Sampler>()) {
-                        params.Push(ctx.Clone(var));
+                for (auto* param : fn->Parameters()) {
+                    if (!param->Type()->IsAnyOf<sem::Texture, sem::Sampler>()) {
+                        params.Push(ctx.Clone(param->Declaration()));
                     }
                 }
                 // Create a new function signature that differs only in the parameter
                 // list.
-                auto symbol = ctx.Clone(src->symbol);
-                auto* return_type = ctx.Clone(src->return_type);
-                auto* body = ctx.Clone(src->body);
-                auto attributes = ctx.Clone(src->attributes);
-                auto return_type_attributes = ctx.Clone(src->return_type_attributes);
+                auto symbol = ctx.Clone(ast_fn->symbol);
+                auto* return_type = ctx.Clone(ast_fn->return_type);
+                auto* body = ctx.Clone(ast_fn->body);
+                auto attributes = ctx.Clone(ast_fn->attributes);
+                auto return_type_attributes = ctx.Clone(ast_fn->return_type_attributes);
                 return ctx.dst->create<ast::Function>(symbol, params, return_type, body,
                                                       std::move(attributes),
                                                       std::move(return_type_attributes));
@@ -327,6 +332,7 @@
         });
 
         ctx.Clone();
+        return Program(std::move(b));
     }
 };
 
@@ -334,15 +340,18 @@
 
 CombineSamplers::~CombineSamplers() = default;
 
-void CombineSamplers::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) const {
+Transform::ApplyResult CombineSamplers::Apply(const Program* src,
+                                              const DataMap& inputs,
+                                              DataMap&) const {
     auto* binding_info = inputs.Get<BindingInfo>();
     if (!binding_info) {
-        ctx.dst->Diagnostics().add_error(
-            diag::System::Transform, "missing transform data for " + std::string(TypeInfo().name));
-        return;
+        ProgramBuilder b;
+        b.Diagnostics().add_error(diag::System::Transform,
+                                  "missing transform data for " + std::string(TypeInfo().name));
+        return Program(std::move(b));
     }
 
-    State(ctx, binding_info).Run();
+    return State(src, binding_info).Run();
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/combine_samplers.h b/src/tint/transform/combine_samplers.h
index 8dfc098..6834abe 100644
--- a/src/tint/transform/combine_samplers.h
+++ b/src/tint/transform/combine_samplers.h
@@ -88,17 +88,13 @@
     /// Destructor
     ~CombineSamplers() override;
 
-  protected:
-    /// The PIMPL state for this transform
-    struct State;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+  private:
+    struct State;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/decompose_memory_access.cc b/src/tint/transform/decompose_memory_access.cc
index 68324af..046583e 100644
--- a/src/tint/transform/decompose_memory_access.cc
+++ b/src/tint/transform/decompose_memory_access.cc
@@ -47,6 +47,18 @@
 
 namespace {
 
+bool ShouldRun(const Program* program) {
+    for (auto* decl : program->AST().GlobalDeclarations()) {
+        if (auto* var = program->Sem().Get<sem::Variable>(decl)) {
+            if (var->AddressSpace() == ast::AddressSpace::kStorage ||
+                var->AddressSpace() == ast::AddressSpace::kUniform) {
+                return true;
+            }
+        }
+    }
+    return false;
+}
+
 /// Offset is a simple ast::Expression builder interface, used to build byte
 /// offsets for storage and uniform buffer accesses.
 struct Offset : Castable<Offset> {
@@ -291,7 +303,7 @@
 
 }  // namespace
 
-/// State holds the current transform state
+/// PIMPL state for the transform
 struct DecomposeMemoryAccess::State {
     /// The clone context
     CloneContext& ctx;
@@ -477,7 +489,7 @@
                         // * Override-expression counts can only be applied to workgroup arrays, and
                         //   this method only handles storage and uniform.
                         // * Runtime-sized arrays are not loadable.
-                        TINT_ICE(Transform, ctx.dst->Diagnostics())
+                        TINT_ICE(Transform, b.Diagnostics())
                             << "unexpected non-constant array count";
                         arr_cnt = 1;
                     }
@@ -578,7 +590,7 @@
                                 // * Override-expression counts can only be applied to workgroup
                                 //   arrays, and this method only handles storage and uniform.
                                 // * Runtime-sized arrays are not storable.
-                                TINT_ICE(Transform, ctx.dst->Diagnostics())
+                                TINT_ICE(Transform, b.Diagnostics())
                                     << "unexpected non-constant array count";
                                 arr_cnt = 1;
                             }
@@ -808,21 +820,16 @@
 DecomposeMemoryAccess::DecomposeMemoryAccess() = default;
 DecomposeMemoryAccess::~DecomposeMemoryAccess() = default;
 
-bool DecomposeMemoryAccess::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* decl : program->AST().GlobalDeclarations()) {
-        if (auto* var = program->Sem().Get<sem::Variable>(decl)) {
-            if (var->AddressSpace() == ast::AddressSpace::kStorage ||
-                var->AddressSpace() == ast::AddressSpace::kUniform) {
-                return true;
-            }
-        }
+Transform::ApplyResult DecomposeMemoryAccess::Apply(const Program* src,
+                                                    const DataMap&,
+                                                    DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
     }
-    return false;
-}
 
-void DecomposeMemoryAccess::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    auto& sem = ctx.src->Sem();
-
+    auto& sem = src->Sem();
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
     State state(ctx);
 
     // Scan the AST nodes for storage and uniform buffer accesses. Complex
@@ -833,7 +840,7 @@
     // Inner-most expression nodes are guaranteed to be visited first because AST
     // nodes are fully immutable and require their children to be constructed
     // first so their pointer can be passed to the parent's initializer.
-    for (auto* node : ctx.src->ASTNodes().Objects()) {
+    for (auto* node : src->ASTNodes().Objects()) {
         if (auto* ident = node->As<ast::IdentifierExpression>()) {
             // X
             if (auto* var = sem.Get<sem::VariableUser>(ident)) {
@@ -1001,6 +1008,7 @@
     }
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/decompose_memory_access.h b/src/tint/transform/decompose_memory_access.h
index 2e92a3a..21c196b 100644
--- a/src/tint/transform/decompose_memory_access.h
+++ b/src/tint/transform/decompose_memory_access.h
@@ -108,20 +108,12 @@
     /// Destructor
     ~DecomposeMemoryAccess() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
-
+  private:
     struct State;
 };
 
diff --git a/src/tint/transform/decompose_strided_array.cc b/src/tint/transform/decompose_strided_array.cc
index e9f51a5..73a6629 100644
--- a/src/tint/transform/decompose_strided_array.cc
+++ b/src/tint/transform/decompose_strided_array.cc
@@ -34,13 +34,7 @@
 
 using DecomposedArrays = std::unordered_map<const sem::Array*, Symbol>;
 
-}  // namespace
-
-DecomposeStridedArray::DecomposeStridedArray() = default;
-
-DecomposeStridedArray::~DecomposeStridedArray() = default;
-
-bool DecomposeStridedArray::ShouldRun(const Program* program, const DataMap&) const {
+bool ShouldRun(const Program* program) {
     for (auto* node : program->ASTNodes().Objects()) {
         if (auto* ast = node->As<ast::Array>()) {
             if (ast::GetAttribute<ast::StrideAttribute>(ast->attributes)) {
@@ -51,8 +45,22 @@
     return false;
 }
 
-void DecomposeStridedArray::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    const auto& sem = ctx.src->Sem();
+}  // namespace
+
+DecomposeStridedArray::DecomposeStridedArray() = default;
+
+DecomposeStridedArray::~DecomposeStridedArray() = default;
+
+Transform::ApplyResult DecomposeStridedArray::Apply(const Program* src,
+                                                    const DataMap&,
+                                                    DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
+    }
+
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+    const auto& sem = src->Sem();
 
     static constexpr const char* kMemberName = "el";
 
@@ -69,23 +77,23 @@
         if (auto* arr = sem.Get(ast)) {
             if (!arr->IsStrideImplicit()) {
                 auto el_ty = utils::GetOrCreate(decomposed, arr, [&] {
-                    auto name = ctx.dst->Symbols().New("strided_arr");
+                    auto name = b.Symbols().New("strided_arr");
                     auto* member_ty = ctx.Clone(ast->type);
-                    auto* member = ctx.dst->Member(kMemberName, member_ty,
-                                                   utils::Vector{
-                                                       ctx.dst->MemberSize(AInt(arr->Stride())),
-                                                   });
-                    ctx.dst->Structure(name, utils::Vector{member});
+                    auto* member = b.Member(kMemberName, member_ty,
+                                            utils::Vector{
+                                                b.MemberSize(AInt(arr->Stride())),
+                                            });
+                    b.Structure(name, utils::Vector{member});
                     return name;
                 });
                 auto* count = ctx.Clone(ast->count);
-                return ctx.dst->ty.array(ctx.dst->ty.type_name(el_ty), count);
+                return b.ty.array(b.ty.type_name(el_ty), count);
             }
             if (ast::GetAttribute<ast::StrideAttribute>(ast->attributes)) {
                 // Strip the @stride attribute
                 auto* ty = ctx.Clone(ast->type);
                 auto* count = ctx.Clone(ast->count);
-                return ctx.dst->ty.array(ty, count);
+                return b.ty.array(ty, count);
             }
         }
         return nullptr;
@@ -96,11 +104,11 @@
     // to insert an additional member accessor for the single structure field.
     // Example: `arr[i]` -> `arr[i].el`
     ctx.ReplaceAll([&](const ast::IndexAccessorExpression* idx) -> const ast::Expression* {
-        if (auto* ty = ctx.src->TypeOf(idx->object)) {
+        if (auto* ty = src->TypeOf(idx->object)) {
             if (auto* arr = ty->UnwrapRef()->As<sem::Array>()) {
                 if (!arr->IsStrideImplicit()) {
                     auto* expr = ctx.CloneWithoutTransform(idx);
-                    return ctx.dst->MemberAccessor(expr, kMemberName);
+                    return b.MemberAccessor(expr, kMemberName);
                 }
             }
         }
@@ -136,21 +144,23 @@
                         if (auto it = decomposed.find(arr); it != decomposed.end()) {
                             args.Reserve(expr->args.Length());
                             for (auto* arg : expr->args) {
-                                args.Push(ctx.dst->Call(it->second, ctx.Clone(arg)));
+                                args.Push(b.Call(it->second, ctx.Clone(arg)));
                             }
                         } else {
                             args = ctx.Clone(expr->args);
                         }
 
-                        return target.type ? ctx.dst->Construct(target.type, std::move(args))
-                                           : ctx.dst->Call(target.name, std::move(args));
+                        return target.type ? b.Construct(target.type, std::move(args))
+                                           : b.Call(target.name, std::move(args));
                     }
                 }
             }
         }
         return nullptr;
     });
+
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/decompose_strided_array.h b/src/tint/transform/decompose_strided_array.h
index 5dbaaa5..9555a9a 100644
--- a/src/tint/transform/decompose_strided_array.h
+++ b/src/tint/transform/decompose_strided_array.h
@@ -35,19 +35,10 @@
     /// Destructor
     ~DecomposeStridedArray() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/decompose_strided_matrix.cc b/src/tint/transform/decompose_strided_matrix.cc
index 91aed43..5494ca2 100644
--- a/src/tint/transform/decompose_strided_matrix.cc
+++ b/src/tint/transform/decompose_strided_matrix.cc
@@ -53,24 +53,25 @@
     };
 };
 
-/// Return type of the callback function of GatherCustomStrideMatrixMembers
-enum GatherResult { kContinue, kStop };
+}  // namespace
 
-/// GatherCustomStrideMatrixMembers scans `program` for all matrix members of
-/// storage and uniform structs, which are of a matrix type, and have a custom
-/// matrix stride attribute. For each matrix member found, `callback` is called.
-/// `callback` is a function with the signature:
-///      GatherResult(const sem::StructMember* member,
-///                   sem::Matrix* matrix,
-///                   uint32_t stride)
-/// If `callback` return GatherResult::kStop, then the scanning will immediately
-/// terminate, and GatherCustomStrideMatrixMembers() will return, otherwise
-/// scanning will continue.
-template <typename F>
-void GatherCustomStrideMatrixMembers(const Program* program, F&& callback) {
-    for (auto* node : program->ASTNodes().Objects()) {
+DecomposeStridedMatrix::DecomposeStridedMatrix() = default;
+
+DecomposeStridedMatrix::~DecomposeStridedMatrix() = default;
+
+Transform::ApplyResult DecomposeStridedMatrix::Apply(const Program* src,
+                                                     const DataMap&,
+                                                     DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
+    // Scan the program for all storage and uniform structure matrix members with
+    // a custom stride attribute. Replace these matrices with an equivalent array,
+    // and populate the `decomposed` map with the members that have been replaced.
+    utils::Hashmap<const ast::StructMember*, MatrixInfo, 8> decomposed;
+    for (auto* node : src->ASTNodes().Objects()) {
         if (auto* str = node->As<ast::Struct>()) {
-            auto* str_ty = program->Sem().Get(str);
+            auto* str_ty = src->Sem().Get(str);
             if (!str_ty->UsedAs(ast::AddressSpace::kUniform) &&
                 !str_ty->UsedAs(ast::AddressSpace::kStorage)) {
                 continue;
@@ -89,46 +90,20 @@
                 if (matrix->ColumnStride() == stride) {
                     continue;
                 }
-                if (callback(member, matrix, stride) == GatherResult::kStop) {
-                    return;
-                }
+                // We've got ourselves a struct member of a matrix type with a custom
+                // stride. Replace this with an array of column vectors.
+                MatrixInfo info{stride, matrix};
+                auto* replacement =
+                    b.Member(member->Offset(), ctx.Clone(member->Name()), info.array(ctx.dst));
+                ctx.Replace(member->Declaration(), replacement);
+                decomposed.Add(member->Declaration(), info);
             }
         }
     }
-}
 
-}  // namespace
-
-DecomposeStridedMatrix::DecomposeStridedMatrix() = default;
-
-DecomposeStridedMatrix::~DecomposeStridedMatrix() = default;
-
-bool DecomposeStridedMatrix::ShouldRun(const Program* program, const DataMap&) const {
-    bool should_run = false;
-    GatherCustomStrideMatrixMembers(program,
-                                    [&](const sem::StructMember*, const sem::Matrix*, uint32_t) {
-                                        should_run = true;
-                                        return GatherResult::kStop;
-                                    });
-    return should_run;
-}
-
-void DecomposeStridedMatrix::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    // Scan the program for all storage and uniform structure matrix members with
-    // a custom stride attribute. Replace these matrices with an equivalent array,
-    // and populate the `decomposed` map with the members that have been replaced.
-    std::unordered_map<const ast::StructMember*, MatrixInfo> decomposed;
-    GatherCustomStrideMatrixMembers(
-        ctx.src, [&](const sem::StructMember* member, const sem::Matrix* matrix, uint32_t stride) {
-            // We've got ourselves a struct member of a matrix type with a custom
-            // stride. Replace this with an array of column vectors.
-            MatrixInfo info{stride, matrix};
-            auto* replacement =
-                ctx.dst->Member(member->Offset(), ctx.Clone(member->Name()), info.array(ctx.dst));
-            ctx.Replace(member->Declaration(), replacement);
-            decomposed.emplace(member->Declaration(), info);
-            return GatherResult::kContinue;
-        });
+    if (decomposed.IsEmpty()) {
+        return SkipTransform;
+    }
 
     // For all expressions where a single matrix column vector was indexed, we can
     // preserve these without calling conversion functions.
@@ -136,12 +111,11 @@
     //   ssbo.mat[2] -> ssbo.mat[2]
     ctx.ReplaceAll(
         [&](const ast::IndexAccessorExpression* expr) -> const ast::IndexAccessorExpression* {
-            if (auto* access = ctx.src->Sem().Get<sem::StructMemberAccess>(expr->object)) {
-                auto it = decomposed.find(access->Member()->Declaration());
-                if (it != decomposed.end()) {
+            if (auto* access = src->Sem().Get<sem::StructMemberAccess>(expr->object)) {
+                if (decomposed.Contains(access->Member()->Declaration())) {
                     auto* obj = ctx.CloneWithoutTransform(expr->object);
                     auto* idx = ctx.Clone(expr->index);
-                    return ctx.dst->IndexAccessor(obj, idx);
+                    return b.IndexAccessor(obj, idx);
                 }
             }
             return nullptr;
@@ -154,39 +128,36 @@
     //   ssbo.mat = mat_to_arr(m)
     std::unordered_map<MatrixInfo, Symbol, MatrixInfo::Hasher> mat_to_arr;
     ctx.ReplaceAll([&](const ast::AssignmentStatement* stmt) -> const ast::Statement* {
-        if (auto* access = ctx.src->Sem().Get<sem::StructMemberAccess>(stmt->lhs)) {
-            auto it = decomposed.find(access->Member()->Declaration());
-            if (it == decomposed.end()) {
-                return nullptr;
+        if (auto* access = src->Sem().Get<sem::StructMemberAccess>(stmt->lhs)) {
+            if (auto* info = decomposed.Find(access->Member()->Declaration())) {
+                auto fn = utils::GetOrCreate(mat_to_arr, *info, [&] {
+                    auto name =
+                        b.Symbols().New("mat" + std::to_string(info->matrix->columns()) + "x" +
+                                        std::to_string(info->matrix->rows()) + "_stride_" +
+                                        std::to_string(info->stride) + "_to_arr");
+
+                    auto matrix = [&] { return CreateASTTypeFor(ctx, info->matrix); };
+                    auto array = [&] { return info->array(ctx.dst); };
+
+                    auto mat = b.Sym("m");
+                    utils::Vector<const ast::Expression*, 4> columns;
+                    for (uint32_t i = 0; i < static_cast<uint32_t>(info->matrix->columns()); i++) {
+                        columns.Push(b.IndexAccessor(mat, u32(i)));
+                    }
+                    b.Func(name,
+                           utils::Vector{
+                               b.Param(mat, matrix()),
+                           },
+                           array(),
+                           utils::Vector{
+                               b.Return(b.Construct(array(), columns)),
+                           });
+                    return name;
+                });
+                auto* lhs = ctx.CloneWithoutTransform(stmt->lhs);
+                auto* rhs = b.Call(fn, ctx.Clone(stmt->rhs));
+                return b.Assign(lhs, rhs);
             }
-            MatrixInfo info = it->second;
-            auto fn = utils::GetOrCreate(mat_to_arr, info, [&] {
-                auto name =
-                    ctx.dst->Symbols().New("mat" + std::to_string(info.matrix->columns()) + "x" +
-                                           std::to_string(info.matrix->rows()) + "_stride_" +
-                                           std::to_string(info.stride) + "_to_arr");
-
-                auto matrix = [&] { return CreateASTTypeFor(ctx, info.matrix); };
-                auto array = [&] { return info.array(ctx.dst); };
-
-                auto mat = ctx.dst->Sym("m");
-                utils::Vector<const ast::Expression*, 4> columns;
-                for (uint32_t i = 0; i < static_cast<uint32_t>(info.matrix->columns()); i++) {
-                    columns.Push(ctx.dst->IndexAccessor(mat, u32(i)));
-                }
-                ctx.dst->Func(name,
-                              utils::Vector{
-                                  ctx.dst->Param(mat, matrix()),
-                              },
-                              array(),
-                              utils::Vector{
-                                  ctx.dst->Return(ctx.dst->Construct(array(), columns)),
-                              });
-                return name;
-            });
-            auto* lhs = ctx.CloneWithoutTransform(stmt->lhs);
-            auto* rhs = ctx.dst->Call(fn, ctx.Clone(stmt->rhs));
-            return ctx.dst->Assign(lhs, rhs);
         }
         return nullptr;
     });
@@ -196,41 +167,40 @@
     //   m = arr_to_mat(ssbo.mat)
     std::unordered_map<MatrixInfo, Symbol, MatrixInfo::Hasher> arr_to_mat;
     ctx.ReplaceAll([&](const ast::MemberAccessorExpression* expr) -> const ast::Expression* {
-        if (auto* access = ctx.src->Sem().Get<sem::StructMemberAccess>(expr)) {
-            auto it = decomposed.find(access->Member()->Declaration());
-            if (it == decomposed.end()) {
-                return nullptr;
+        if (auto* access = src->Sem().Get<sem::StructMemberAccess>(expr)) {
+            if (auto* info = decomposed.Find(access->Member()->Declaration())) {
+                auto fn = utils::GetOrCreate(arr_to_mat, *info, [&] {
+                    auto name =
+                        b.Symbols().New("arr_to_mat" + std::to_string(info->matrix->columns()) +
+                                        "x" + std::to_string(info->matrix->rows()) + "_stride_" +
+                                        std::to_string(info->stride));
+
+                    auto matrix = [&] { return CreateASTTypeFor(ctx, info->matrix); };
+                    auto array = [&] { return info->array(ctx.dst); };
+
+                    auto arr = b.Sym("arr");
+                    utils::Vector<const ast::Expression*, 4> columns;
+                    for (uint32_t i = 0; i < static_cast<uint32_t>(info->matrix->columns()); i++) {
+                        columns.Push(b.IndexAccessor(arr, u32(i)));
+                    }
+                    b.Func(name,
+                           utils::Vector{
+                               b.Param(arr, array()),
+                           },
+                           matrix(),
+                           utils::Vector{
+                               b.Return(b.Construct(matrix(), columns)),
+                           });
+                    return name;
+                });
+                return b.Call(fn, ctx.CloneWithoutTransform(expr));
             }
-            MatrixInfo info = it->second;
-            auto fn = utils::GetOrCreate(arr_to_mat, info, [&] {
-                auto name = ctx.dst->Symbols().New(
-                    "arr_to_mat" + std::to_string(info.matrix->columns()) + "x" +
-                    std::to_string(info.matrix->rows()) + "_stride_" + std::to_string(info.stride));
-
-                auto matrix = [&] { return CreateASTTypeFor(ctx, info.matrix); };
-                auto array = [&] { return info.array(ctx.dst); };
-
-                auto arr = ctx.dst->Sym("arr");
-                utils::Vector<const ast::Expression*, 4> columns;
-                for (uint32_t i = 0; i < static_cast<uint32_t>(info.matrix->columns()); i++) {
-                    columns.Push(ctx.dst->IndexAccessor(arr, u32(i)));
-                }
-                ctx.dst->Func(name,
-                              utils::Vector{
-                                  ctx.dst->Param(arr, array()),
-                              },
-                              matrix(),
-                              utils::Vector{
-                                  ctx.dst->Return(ctx.dst->Construct(matrix(), columns)),
-                              });
-                return name;
-            });
-            return ctx.dst->Call(fn, ctx.CloneWithoutTransform(expr));
         }
         return nullptr;
     });
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/decompose_strided_matrix.h b/src/tint/transform/decompose_strided_matrix.h
index 40e9c3e..947dfc6 100644
--- a/src/tint/transform/decompose_strided_matrix.h
+++ b/src/tint/transform/decompose_strided_matrix.h
@@ -35,19 +35,10 @@
     /// Destructor
     ~DecomposeStridedMatrix() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/disable_uniformity_analysis.cc b/src/tint/transform/disable_uniformity_analysis.cc
index 918b1f1..ffd0b18 100644
--- a/src/tint/transform/disable_uniformity_analysis.cc
+++ b/src/tint/transform/disable_uniformity_analysis.cc
@@ -27,14 +27,20 @@
 
 DisableUniformityAnalysis::~DisableUniformityAnalysis() = default;
 
-bool DisableUniformityAnalysis::ShouldRun(const Program* program, const DataMap&) const {
-    return !program->Sem().Module()->Extensions().Contains(
-        ast::Extension::kChromiumDisableUniformityAnalysis);
-}
+Transform::ApplyResult DisableUniformityAnalysis::Apply(const Program* src,
+                                                        const DataMap&,
+                                                        DataMap&) const {
+    if (src->Sem().Module()->Extensions().Contains(
+            ast::Extension::kChromiumDisableUniformityAnalysis)) {
+        return SkipTransform;
+    }
 
-void DisableUniformityAnalysis::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    ctx.dst->Enable(ast::Extension::kChromiumDisableUniformityAnalysis);
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+    b.Enable(ast::Extension::kChromiumDisableUniformityAnalysis);
+
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/disable_uniformity_analysis.h b/src/tint/transform/disable_uniformity_analysis.h
index 3c9fb53..a9922af 100644
--- a/src/tint/transform/disable_uniformity_analysis.h
+++ b/src/tint/transform/disable_uniformity_analysis.h
@@ -27,19 +27,10 @@
     /// Destructor
     ~DisableUniformityAnalysis() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/expand_compound_assignment.cc b/src/tint/transform/expand_compound_assignment.cc
index f15e28c..9fa81dd 100644
--- a/src/tint/transform/expand_compound_assignment.cc
+++ b/src/tint/transform/expand_compound_assignment.cc
@@ -31,11 +31,9 @@
 
 namespace tint::transform {
 
-ExpandCompoundAssignment::ExpandCompoundAssignment() = default;
+namespace {
 
-ExpandCompoundAssignment::~ExpandCompoundAssignment() = default;
-
-bool ExpandCompoundAssignment::ShouldRun(const Program* program, const DataMap&) const {
+bool ShouldRun(const Program* program) {
     for (auto* node : program->ASTNodes().Objects()) {
         if (node->IsAnyOf<ast::CompoundAssignmentStatement, ast::IncrementDecrementStatement>()) {
             return true;
@@ -44,21 +42,10 @@
     return false;
 }
 
-namespace {
+}  // namespace
 
-/// Internal class used to collect statement expansions during the transform.
-class State {
-  private:
-    /// The clone context.
-    CloneContext& ctx;
-
-    /// The program builder.
-    ProgramBuilder& b;
-
-    /// The HoistToDeclBefore helper instance.
-    HoistToDeclBefore hoist_to_decl_before;
-
-  public:
+/// PIMPL state for the transform
+struct ExpandCompoundAssignment::State {
     /// Constructor
     /// @param context the clone context
     explicit State(CloneContext& context) : ctx(context), b(*ctx.dst), hoist_to_decl_before(ctx) {}
@@ -158,15 +145,32 @@
         ctx.Replace(stmt, b.Assign(new_lhs(), value));
     }
 
-    /// Finalize the transformation and clone the module.
-    void Finalize() { ctx.Clone(); }
+  private:
+    /// The clone context.
+    CloneContext& ctx;
+
+    /// The program builder.
+    ProgramBuilder& b;
+
+    /// The HoistToDeclBefore helper instance.
+    HoistToDeclBefore hoist_to_decl_before;
 };
 
-}  // namespace
+ExpandCompoundAssignment::ExpandCompoundAssignment() = default;
 
-void ExpandCompoundAssignment::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+ExpandCompoundAssignment::~ExpandCompoundAssignment() = default;
+
+Transform::ApplyResult ExpandCompoundAssignment::Apply(const Program* src,
+                                                       const DataMap&,
+                                                       DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
+    }
+
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
     State state(ctx);
-    for (auto* node : ctx.src->ASTNodes().Objects()) {
+    for (auto* node : src->ASTNodes().Objects()) {
         if (auto* assign = node->As<ast::CompoundAssignmentStatement>()) {
             state.Expand(assign, assign->lhs, ctx.Clone(assign->rhs), assign->op);
         } else if (auto* inc_dec = node->As<ast::IncrementDecrementStatement>()) {
@@ -175,7 +179,9 @@
             state.Expand(inc_dec, inc_dec->lhs, ctx.dst->Expr(1_a), op);
         }
     }
-    state.Finalize();
+
+    ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/expand_compound_assignment.h b/src/tint/transform/expand_compound_assignment.h
index 1081df7..6b299c5 100644
--- a/src/tint/transform/expand_compound_assignment.h
+++ b/src/tint/transform/expand_compound_assignment.h
@@ -45,19 +45,13 @@
     /// Destructor
     ~ExpandCompoundAssignment() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+  private:
+    struct State;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/first_index_offset.cc b/src/tint/transform/first_index_offset.cc
index cafca32..eb698be 100644
--- a/src/tint/transform/first_index_offset.cc
+++ b/src/tint/transform/first_index_offset.cc
@@ -35,6 +35,15 @@
 constexpr char kFirstVertexName[] = "first_vertex_index";
 constexpr char kFirstInstanceName[] = "first_instance_index";
 
+bool ShouldRun(const Program* program) {
+    for (auto* fn : program->AST().Functions()) {
+        if (fn->PipelineStage() == ast::PipelineStage::kVertex) {
+            return true;
+        }
+    }
+    return false;
+}
+
 }  // namespace
 
 FirstIndexOffset::BindingPoint::BindingPoint() = default;
@@ -49,16 +58,16 @@
 FirstIndexOffset::FirstIndexOffset() = default;
 FirstIndexOffset::~FirstIndexOffset() = default;
 
-bool FirstIndexOffset::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* fn : program->AST().Functions()) {
-        if (fn->PipelineStage() == ast::PipelineStage::kVertex) {
-            return true;
-        }
+Transform::ApplyResult FirstIndexOffset::Apply(const Program* src,
+                                               const DataMap& inputs,
+                                               DataMap& outputs) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
     }
-    return false;
-}
 
-void FirstIndexOffset::Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     // Get the uniform buffer binding point
     uint32_t ub_binding = binding_;
     uint32_t ub_group = group_;
@@ -115,17 +124,17 @@
     if (has_vertex_or_instance_index) {
         // Add uniform buffer members and calculate byte offsets
         utils::Vector<const ast::StructMember*, 8> members;
-        members.Push(ctx.dst->Member(kFirstVertexName, ctx.dst->ty.u32()));
-        members.Push(ctx.dst->Member(kFirstInstanceName, ctx.dst->ty.u32()));
-        auto* struct_ = ctx.dst->Structure(ctx.dst->Sym(), std::move(members));
+        members.Push(b.Member(kFirstVertexName, b.ty.u32()));
+        members.Push(b.Member(kFirstInstanceName, b.ty.u32()));
+        auto* struct_ = b.Structure(b.Sym(), std::move(members));
 
         // Create a global to hold the uniform buffer
-        Symbol buffer_name = ctx.dst->Sym();
-        ctx.dst->GlobalVar(buffer_name, ctx.dst->ty.Of(struct_), ast::AddressSpace::kUniform,
-                           utils::Vector{
-                               ctx.dst->Binding(AInt(ub_binding)),
-                               ctx.dst->Group(AInt(ub_group)),
-                           });
+        Symbol buffer_name = b.Sym();
+        b.GlobalVar(buffer_name, b.ty.Of(struct_), ast::AddressSpace::kUniform,
+                    utils::Vector{
+                        b.Binding(AInt(ub_binding)),
+                        b.Group(AInt(ub_group)),
+                    });
 
         // Fix up all references to the builtins with the offsets
         ctx.ReplaceAll([=, &ctx](const ast::Expression* expr) -> const ast::Expression* {
@@ -150,9 +159,10 @@
         });
     }
 
-    ctx.Clone();
-
     outputs.Add<Data>(has_vertex_or_instance_index);
+
+    ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/first_index_offset.h b/src/tint/transform/first_index_offset.h
index 04758cd..f84d811 100644
--- a/src/tint/transform/first_index_offset.h
+++ b/src/tint/transform/first_index_offset.h
@@ -103,19 +103,10 @@
     /// Destructor
     ~FirstIndexOffset() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
   private:
     uint32_t binding_ = 0;
diff --git a/src/tint/transform/for_loop_to_loop.cc b/src/tint/transform/for_loop_to_loop.cc
index e585790..63ccb12 100644
--- a/src/tint/transform/for_loop_to_loop.cc
+++ b/src/tint/transform/for_loop_to_loop.cc
@@ -14,17 +14,17 @@
 
 #include "src/tint/transform/for_loop_to_loop.h"
 
+#include <utility>
+
 #include "src/tint/ast/break_statement.h"
 #include "src/tint/program_builder.h"
 
 TINT_INSTANTIATE_TYPEINFO(tint::transform::ForLoopToLoop);
 
 namespace tint::transform {
-ForLoopToLoop::ForLoopToLoop() = default;
+namespace {
 
-ForLoopToLoop::~ForLoopToLoop() = default;
-
-bool ForLoopToLoop::ShouldRun(const Program* program, const DataMap&) const {
+bool ShouldRun(const Program* program) {
     for (auto* node : program->ASTNodes().Objects()) {
         if (node->Is<ast::ForLoopStatement>()) {
             return true;
@@ -33,19 +33,31 @@
     return false;
 }
 
-void ForLoopToLoop::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+}  // namespace
+
+ForLoopToLoop::ForLoopToLoop() = default;
+
+ForLoopToLoop::~ForLoopToLoop() = default;
+
+Transform::ApplyResult ForLoopToLoop::Apply(const Program* src, const DataMap&, DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
+    }
+
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     ctx.ReplaceAll([&](const ast::ForLoopStatement* for_loop) -> const ast::Statement* {
         utils::Vector<const ast::Statement*, 8> stmts;
         if (auto* cond = for_loop->condition) {
             // !condition
-            auto* not_cond =
-                ctx.dst->create<ast::UnaryOpExpression>(ast::UnaryOp::kNot, ctx.Clone(cond));
+            auto* not_cond = b.Not(ctx.Clone(cond));
 
             // { break; }
-            auto* break_body = ctx.dst->Block(ctx.dst->create<ast::BreakStatement>());
+            auto* break_body = b.Block(b.Break());
 
             // if (!condition) { break; }
-            stmts.Push(ctx.dst->If(not_cond, break_body));
+            stmts.Push(b.If(not_cond, break_body));
         }
         for (auto* stmt : for_loop->body->statements) {
             stmts.Push(ctx.Clone(stmt));
@@ -53,20 +65,21 @@
 
         const ast::BlockStatement* continuing = nullptr;
         if (auto* cont = for_loop->continuing) {
-            continuing = ctx.dst->Block(ctx.Clone(cont));
+            continuing = b.Block(ctx.Clone(cont));
         }
 
-        auto* body = ctx.dst->Block(stmts);
-        auto* loop = ctx.dst->create<ast::LoopStatement>(body, continuing);
+        auto* body = b.Block(stmts);
+        auto* loop = b.Loop(body, continuing);
 
         if (auto* init = for_loop->initializer) {
-            return ctx.dst->Block(ctx.Clone(init), loop);
+            return b.Block(ctx.Clone(init), loop);
         }
 
         return loop;
     });
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/for_loop_to_loop.h b/src/tint/transform/for_loop_to_loop.h
index 5ab690a..fe3db97 100644
--- a/src/tint/transform/for_loop_to_loop.h
+++ b/src/tint/transform/for_loop_to_loop.h
@@ -29,19 +29,10 @@
     /// Destructor
     ~ForLoopToLoop() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/localize_struct_array_assignment.cc b/src/tint/transform/localize_struct_array_assignment.cc
index 8077393..bfe8865 100644
--- a/src/tint/transform/localize_struct_array_assignment.cc
+++ b/src/tint/transform/localize_struct_array_assignment.cc
@@ -32,70 +32,15 @@
 
 namespace tint::transform {
 
-/// Private implementation of LocalizeStructArrayAssignment transform
-class LocalizeStructArrayAssignment::State {
-  private:
-    CloneContext& ctx;
-    ProgramBuilder& b;
-
-    /// Returns true if `expr` contains an index accessor expression to a
-    /// structure member of array type.
-    bool ContainsStructArrayIndex(const ast::Expression* expr) {
-        bool result = false;
-        ast::TraverseExpressions(
-            expr, b.Diagnostics(), [&](const ast::IndexAccessorExpression* ia) {
-                // Indexing using a runtime value?
-                auto* idx_sem = ctx.src->Sem().Get(ia->index);
-                if (!idx_sem->ConstantValue()) {
-                    // Indexing a member access expr?
-                    if (auto* ma = ia->object->As<ast::MemberAccessorExpression>()) {
-                        // That accesses an array?
-                        if (ctx.src->TypeOf(ma)->UnwrapRef()->Is<sem::Array>()) {
-                            result = true;
-                            return ast::TraverseAction::Stop;
-                        }
-                    }
-                }
-                return ast::TraverseAction::Descend;
-            });
-
-        return result;
-    }
-
-    // Returns the type and address space of the originating variable of the lhs
-    // of the assignment statement.
-    // See https://www.w3.org/TR/WGSL/#originating-variable-section
-    std::pair<const sem::Type*, ast::AddressSpace> GetOriginatingTypeAndAddressSpace(
-        const ast::AssignmentStatement* assign_stmt) {
-        auto* source_var = ctx.src->Sem().Get(assign_stmt->lhs)->SourceVariable();
-        if (!source_var) {
-            TINT_ICE(Transform, b.Diagnostics())
-                << "Unable to determine originating variable for lhs of assignment "
-                   "statement";
-            return {};
-        }
-
-        auto* type = source_var->Type();
-        if (auto* ref = type->As<sem::Reference>()) {
-            return {ref->StoreType(), ref->AddressSpace()};
-        } else if (auto* ptr = type->As<sem::Pointer>()) {
-            return {ptr->StoreType(), ptr->AddressSpace()};
-        }
-
-        TINT_ICE(Transform, b.Diagnostics())
-            << "Expecting to find variable of type pointer or reference on lhs "
-               "of assignment statement";
-        return {};
-    }
-
-  public:
+/// PIMPL state for the transform
+struct LocalizeStructArrayAssignment::State {
     /// Constructor
-    /// @param ctx_in the CloneContext primed with the input program and
-    /// ProgramBuilder
-    explicit State(CloneContext& ctx_in) : ctx(ctx_in), b(*ctx_in.dst) {}
+    /// @param program the source program
+    explicit State(const Program* program) : src(program) {}
 
     /// Runs the transform
-    void Run() {
+    /// @returns the new program or SkipTransform if the transform is not required
+    ApplyResult Run() {
         struct Shared {
             bool process_nested_nodes = false;
             utils::Vector<const ast::Statement*, 4> insert_before_stmts;
@@ -189,6 +134,65 @@
             });
 
         ctx.Clone();
+        return Program(std::move(b));
+    }
+
+  private:
+    /// The source program
+    const Program* const src;
+    /// The target program builder
+    ProgramBuilder b;
+    /// The clone context
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
+
+    /// Returns true if `expr` contains an index accessor expression to a
+    /// structure member of array type.
+    bool ContainsStructArrayIndex(const ast::Expression* expr) {
+        bool result = false;
+        ast::TraverseExpressions(
+            expr, b.Diagnostics(), [&](const ast::IndexAccessorExpression* ia) {
+                // Indexing using a runtime value?
+                auto* idx_sem = src->Sem().Get(ia->index);
+                if (!idx_sem->ConstantValue()) {
+                    // Indexing a member access expr?
+                    if (auto* ma = ia->object->As<ast::MemberAccessorExpression>()) {
+                        // That accesses an array?
+                        if (src->TypeOf(ma)->UnwrapRef()->Is<sem::Array>()) {
+                            result = true;
+                            return ast::TraverseAction::Stop;
+                        }
+                    }
+                }
+                return ast::TraverseAction::Descend;
+            });
+
+        return result;
+    }
+
+    // Returns the type and address space of the originating variable of the lhs
+    // of the assignment statement.
+    // See https://www.w3.org/TR/WGSL/#originating-variable-section
+    std::pair<const sem::Type*, ast::AddressSpace> GetOriginatingTypeAndAddressSpace(
+        const ast::AssignmentStatement* assign_stmt) {
+        auto* source_var = src->Sem().Get(assign_stmt->lhs)->SourceVariable();
+        if (!source_var) {
+            TINT_ICE(Transform, b.Diagnostics())
+                << "Unable to determine originating variable for lhs of assignment "
+                   "statement";
+            return {};
+        }
+
+        auto* type = source_var->Type();
+        if (auto* ref = type->As<sem::Reference>()) {
+            return {ref->StoreType(), ref->AddressSpace()};
+        } else if (auto* ptr = type->As<sem::Pointer>()) {
+            return {ptr->StoreType(), ptr->AddressSpace()};
+        }
+
+        TINT_ICE(Transform, b.Diagnostics())
+            << "Expecting to find variable of type pointer or reference on lhs "
+               "of assignment statement";
+        return {};
     }
 };
 
@@ -196,9 +200,10 @@
 
 LocalizeStructArrayAssignment::~LocalizeStructArrayAssignment() = default;
 
-void LocalizeStructArrayAssignment::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    State state(ctx);
-    state.Run();
+Transform::ApplyResult LocalizeStructArrayAssignment::Apply(const Program* src,
+                                                            const DataMap&,
+                                                            DataMap&) const {
+    return State{src}.Run();
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/localize_struct_array_assignment.h b/src/tint/transform/localize_struct_array_assignment.h
index 130f8cc..169e33c 100644
--- a/src/tint/transform/localize_struct_array_assignment.h
+++ b/src/tint/transform/localize_struct_array_assignment.h
@@ -36,17 +36,13 @@
     /// Destructor
     ~LocalizeStructArrayAssignment() override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
   private:
-    class State;
+    struct State;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/manager.cc b/src/tint/transform/manager.cc
index 4e83320..79603c8 100644
--- a/src/tint/transform/manager.cc
+++ b/src/tint/transform/manager.cc
@@ -31,9 +31,9 @@
 Manager::Manager() = default;
 Manager::~Manager() = default;
 
-Output Manager::Run(const Program* program, const DataMap& data) const {
-    const Program* in = program;
-
+Transform::ApplyResult Manager::Apply(const Program* program,
+                                      const DataMap& inputs,
+                                      DataMap& outputs) const {
 #if TINT_PRINT_PROGRAM_FOR_EACH_TRANSFORM
     auto print_program = [&](const char* msg, const Transform* transform) {
         auto wgsl = Program::printer(in);
@@ -46,34 +46,30 @@
     };
 #endif
 
-    Output out;
+    std::optional<Program> output;
+
     for (const auto& transform : transforms_) {
-        if (!transform->ShouldRun(in, data)) {
-            TINT_IF_PRINT_PROGRAM(std::cout << "Skipping " << transform->TypeInfo().name
-                                            << std::endl);
-            continue;
-        }
         TINT_IF_PRINT_PROGRAM(print_program("Input to", transform.get()));
 
-        auto res = transform->Run(in, data);
-        out.program = std::move(res.program);
-        out.data.Add(std::move(res.data));
-        in = &out.program;
-        if (!in->IsValid()) {
-            TINT_IF_PRINT_PROGRAM(print_program("Invalid output of", transform.get()));
-            return out;
-        }
+        if (auto result = transform->Apply(program, inputs, outputs)) {
+            output.emplace(std::move(result.value()));
+            program = &output.value();
 
-        if (transform == transforms_.back()) {
-            TINT_IF_PRINT_PROGRAM(print_program("Output of", transform.get()));
+            if (!program->IsValid()) {
+                TINT_IF_PRINT_PROGRAM(print_program("Invalid output of", transform.get()));
+                break;
+            }
+
+            if (transform == transforms_.back()) {
+                TINT_IF_PRINT_PROGRAM(print_program("Output of", transform.get()));
+            }
+        } else {
+            TINT_IF_PRINT_PROGRAM(std::cout << "Skipped " << transform->TypeInfo().name
+                                            << std::endl);
         }
     }
 
-    if (program == in) {
-        out.program = program->Clone();
-    }
-
-    return out;
+    return output;
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/manager.h b/src/tint/transform/manager.h
index 9d4049f..64ca847 100644
--- a/src/tint/transform/manager.h
+++ b/src/tint/transform/manager.h
@@ -47,11 +47,10 @@
         transforms_.emplace_back(std::make_unique<T>(std::forward<ARGS>(args)...));
     }
 
-    /// Runs the transforms on `program`, returning the transformation result.
-    /// @param program the source program to transform
-    /// @param data optional extra transform-specific input data
-    /// @returns the transformed program and diagnostics
-    Output Run(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
   private:
     std::vector<std::unique_ptr<Transform>> transforms_;
diff --git a/src/tint/transform/merge_return.cc b/src/tint/transform/merge_return.cc
index aec6b6d..2b45b73 100644
--- a/src/tint/transform/merge_return.cc
+++ b/src/tint/transform/merge_return.cc
@@ -65,15 +65,6 @@
 
 MergeReturn::~MergeReturn() = default;
 
-bool MergeReturn::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* func : program->AST().Functions()) {
-        if (NeedsTransform(program, func)) {
-            return true;
-        }
-    }
-    return false;
-}
-
 namespace {
 
 /// Internal class used to during the transform.
@@ -223,7 +214,12 @@
 
 }  // namespace
 
-void MergeReturn::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+Transform::ApplyResult MergeReturn::Apply(const Program* src, const DataMap&, DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
+    bool made_changes = false;
+
     for (auto* func : ctx.src->AST().Functions()) {
         if (!NeedsTransform(ctx.src, func)) {
             continue;
@@ -231,9 +227,15 @@
 
         State state(ctx, func);
         state.ProcessStatement(func->body);
+        made_changes = true;
+    }
+
+    if (!made_changes) {
+        return SkipTransform;
     }
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/merge_return.h b/src/tint/transform/merge_return.h
index 1334a5c..f6db5c2 100644
--- a/src/tint/transform/merge_return.h
+++ b/src/tint/transform/merge_return.h
@@ -27,19 +27,10 @@
     /// Destructor
     ~MergeReturn() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/module_scope_var_to_entry_point_param.cc b/src/tint/transform/module_scope_var_to_entry_point_param.cc
index f9c11e5..16a622e 100644
--- a/src/tint/transform/module_scope_var_to_entry_point_param.cc
+++ b/src/tint/transform/module_scope_var_to_entry_point_param.cc
@@ -38,6 +38,15 @@
 // The name of the struct member for arrays that are wrapped in structures.
 const char* kWrappedArrayMemberName = "arr";
 
+bool ShouldRun(const Program* program) {
+    for (auto* decl : program->AST().GlobalDeclarations()) {
+        if (decl->Is<ast::Variable>()) {
+            return true;
+        }
+    }
+    return false;
+}
+
 // Returns `true` if `type` is or contains a matrix type.
 bool ContainsMatrix(const sem::Type* type) {
     type = type->UnwrapRef();
@@ -56,7 +65,7 @@
 }
 }  // namespace
 
-/// State holds the current transform state.
+/// PIMPL state for the transform
 struct ModuleScopeVarToEntryPointParam::State {
     /// The clone context.
     CloneContext& ctx;
@@ -501,19 +510,20 @@
 
 ModuleScopeVarToEntryPointParam::~ModuleScopeVarToEntryPointParam() = default;
 
-bool ModuleScopeVarToEntryPointParam::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* decl : program->AST().GlobalDeclarations()) {
-        if (decl->Is<ast::Variable>()) {
-            return true;
-        }
+Transform::ApplyResult ModuleScopeVarToEntryPointParam::Apply(const Program* src,
+                                                              const DataMap&,
+                                                              DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
     }
-    return false;
-}
 
-void ModuleScopeVarToEntryPointParam::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
     State state{ctx};
     state.Process();
+
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/module_scope_var_to_entry_point_param.h b/src/tint/transform/module_scope_var_to_entry_point_param.h
index 75bdaf3..377151f 100644
--- a/src/tint/transform/module_scope_var_to_entry_point_param.h
+++ b/src/tint/transform/module_scope_var_to_entry_point_param.h
@@ -69,20 +69,12 @@
     /// Destructor
     ~ModuleScopeVarToEntryPointParam() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
-
+  private:
     struct State;
 };
 
diff --git a/src/tint/transform/multiplanar_external_texture.cc b/src/tint/transform/multiplanar_external_texture.cc
index 002b858..c3ebf4a 100644
--- a/src/tint/transform/multiplanar_external_texture.cc
+++ b/src/tint/transform/multiplanar_external_texture.cc
@@ -31,6 +31,17 @@
 namespace tint::transform {
 namespace {
 
+bool ShouldRun(const Program* program) {
+    for (auto* node : program->ASTNodes().Objects()) {
+        if (auto* ty = node->As<ast::Type>()) {
+            if (program->Sem().Get<sem::ExternalTexture>(ty)) {
+                return true;
+            }
+        }
+    }
+    return false;
+}
+
 /// This struct stores symbols for new bindings created as a result of transforming a
 /// texture_external instance.
 struct NewBindingSymbols {
@@ -40,7 +51,7 @@
 };
 }  // namespace
 
-/// State holds the current transform state
+/// PIMPL state for the transform
 struct MultiplanarExternalTexture::State {
     /// The clone context.
     CloneContext& ctx;
@@ -537,30 +548,26 @@
 MultiplanarExternalTexture::MultiplanarExternalTexture() = default;
 MultiplanarExternalTexture::~MultiplanarExternalTexture() = default;
 
-bool MultiplanarExternalTexture::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* node : program->ASTNodes().Objects()) {
-        if (auto* ty = node->As<ast::Type>()) {
-            if (program->Sem().Get<sem::ExternalTexture>(ty)) {
-                return true;
-            }
-        }
-    }
-    return false;
-}
-
 // Within this transform, an instance of a texture_external binding is unpacked into two
 // texture_2d<f32> bindings representing two possible planes of a single texture and a uniform
 // buffer binding representing a struct of parameters. Calls to texture builtins that contain a
 // texture_external parameter will be transformed into a newly generated version of the function,
 // which can perform the desired operation on a single RGBA plane or on separate Y and UV planes.
-void MultiplanarExternalTexture::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) const {
+Transform::ApplyResult MultiplanarExternalTexture::Apply(const Program* src,
+                                                         const DataMap& inputs,
+                                                         DataMap&) const {
     auto* new_binding_points = inputs.Get<NewBindingPoints>();
 
+    if (!ShouldRun(src)) {
+        return SkipTransform;
+    }
+
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
     if (!new_binding_points) {
-        ctx.dst->Diagnostics().add_error(
-            diag::System::Transform,
-            "missing new binding point data for " + std::string(TypeInfo().name));
-        return;
+        b.Diagnostics().add_error(diag::System::Transform, "missing new binding point data for " +
+                                                               std::string(TypeInfo().name));
+        return Program(std::move(b));
     }
 
     State state(ctx, new_binding_points);
@@ -568,6 +575,7 @@
     state.Process();
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/multiplanar_external_texture.h b/src/tint/transform/multiplanar_external_texture.h
index a10fed4..695e38c 100644
--- a/src/tint/transform/multiplanar_external_texture.h
+++ b/src/tint/transform/multiplanar_external_texture.h
@@ -80,21 +80,13 @@
     /// Destructor
     ~MultiplanarExternalTexture() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-  protected:
+  private:
     struct State;
-
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/multiplanar_external_texture_test.cc b/src/tint/transform/multiplanar_external_texture_test.cc
index dacbb1e..4416d35 100644
--- a/src/tint/transform/multiplanar_external_texture_test.cc
+++ b/src/tint/transform/multiplanar_external_texture_test.cc
@@ -23,7 +23,11 @@
 TEST_F(MultiplanarExternalTextureTest, ShouldRunEmptyModule) {
     auto* src = R"()";
 
-    EXPECT_FALSE(ShouldRun<MultiplanarExternalTexture>(src));
+    DataMap data;
+    data.Add<MultiplanarExternalTexture::NewBindingPoints>(
+        MultiplanarExternalTexture::BindingsMap{{{0, 0}, {{0, 1}, {0, 2}}}});
+
+    EXPECT_FALSE(ShouldRun<MultiplanarExternalTexture>(src, data));
 }
 
 TEST_F(MultiplanarExternalTextureTest, ShouldRunHasExternalTextureAlias) {
@@ -31,14 +35,22 @@
 type ET = texture_external;
 )";
 
-    EXPECT_TRUE(ShouldRun<MultiplanarExternalTexture>(src));
+    DataMap data;
+    data.Add<MultiplanarExternalTexture::NewBindingPoints>(
+        MultiplanarExternalTexture::BindingsMap{{{0, 0}, {{0, 1}, {0, 2}}}});
+
+    EXPECT_TRUE(ShouldRun<MultiplanarExternalTexture>(src, data));
 }
 TEST_F(MultiplanarExternalTextureTest, ShouldRunHasExternalTextureGlobal) {
     auto* src = R"(
 @group(0) @binding(0) var ext_tex : texture_external;
 )";
 
-    EXPECT_TRUE(ShouldRun<MultiplanarExternalTexture>(src));
+    DataMap data;
+    data.Add<MultiplanarExternalTexture::NewBindingPoints>(
+        MultiplanarExternalTexture::BindingsMap{{{0, 0}, {{0, 1}, {0, 2}}}});
+
+    EXPECT_TRUE(ShouldRun<MultiplanarExternalTexture>(src, data));
 }
 
 TEST_F(MultiplanarExternalTextureTest, ShouldRunHasExternalTextureParam) {
@@ -46,7 +58,11 @@
 fn f(ext_tex : texture_external) {}
 )";
 
-    EXPECT_TRUE(ShouldRun<MultiplanarExternalTexture>(src));
+    DataMap data;
+    data.Add<MultiplanarExternalTexture::NewBindingPoints>(
+        MultiplanarExternalTexture::BindingsMap{{{0, 0}, {{0, 1}, {0, 2}}}});
+
+    EXPECT_TRUE(ShouldRun<MultiplanarExternalTexture>(src, data));
 }
 
 // Running the transform without passing in data for the new bindings should result in an error.
diff --git a/src/tint/transform/num_workgroups_from_uniform.cc b/src/tint/transform/num_workgroups_from_uniform.cc
index 2122f07..e6681ca 100644
--- a/src/tint/transform/num_workgroups_from_uniform.cc
+++ b/src/tint/transform/num_workgroups_from_uniform.cc
@@ -29,6 +29,18 @@
 
 namespace tint::transform {
 namespace {
+
+bool ShouldRun(const Program* program) {
+    for (auto* node : program->ASTNodes().Objects()) {
+        if (auto* attr = node->As<ast::BuiltinAttribute>()) {
+            if (attr->builtin == ast::BuiltinValue::kNumWorkgroups) {
+                return true;
+            }
+        }
+    }
+    return false;
+}
+
 /// Accessor describes the identifiers used in a member accessor that is being
 /// used to retrieve the num_workgroups builtin from a parameter.
 struct Accessor {
@@ -44,41 +56,40 @@
         size_t operator()(const Accessor& a) const { return utils::Hash(a.param, a.member); }
     };
 };
+
 }  // namespace
 
 NumWorkgroupsFromUniform::NumWorkgroupsFromUniform() = default;
 NumWorkgroupsFromUniform::~NumWorkgroupsFromUniform() = default;
 
-bool NumWorkgroupsFromUniform::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* node : program->ASTNodes().Objects()) {
-        if (auto* attr = node->As<ast::BuiltinAttribute>()) {
-            if (attr->builtin == ast::BuiltinValue::kNumWorkgroups) {
-                return true;
-            }
-        }
-    }
-    return false;
-}
+Transform::ApplyResult NumWorkgroupsFromUniform::Apply(const Program* src,
+                                                       const DataMap& inputs,
+                                                       DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
 
-void NumWorkgroupsFromUniform::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) const {
     auto* cfg = inputs.Get<Config>();
     if (cfg == nullptr) {
-        ctx.dst->Diagnostics().add_error(
-            diag::System::Transform, "missing transform data for " + std::string(TypeInfo().name));
-        return;
+        b.Diagnostics().add_error(diag::System::Transform,
+                                  "missing transform data for " + std::string(TypeInfo().name));
+        return Program(std::move(b));
+    }
+
+    if (!ShouldRun(src)) {
+        return SkipTransform;
     }
 
     const char* kNumWorkgroupsMemberName = "num_workgroups";
 
     // Find all entry point parameters that declare the num_workgroups builtin.
     std::unordered_set<Accessor, Accessor::Hasher> to_replace;
-    for (auto* func : ctx.src->AST().Functions()) {
+    for (auto* func : src->AST().Functions()) {
         // num_workgroups is only valid for compute stages.
         if (func->PipelineStage() != ast::PipelineStage::kCompute) {
             continue;
         }
 
-        for (auto* param : ctx.src->Sem().Get(func)->Parameters()) {
+        for (auto* param : src->Sem().Get(func)->Parameters()) {
             // Because the CanonicalizeEntryPointIO transform has been run, builtins
             // will only appear as struct members.
             auto* str = param->Type()->As<sem::Struct>();
@@ -108,7 +119,7 @@
                 // If this is the only member, remove the struct and parameter too.
                 if (str->Members().size() == 1) {
                     ctx.Remove(func->params, param->Declaration());
-                    ctx.Remove(ctx.src->AST().GlobalDeclarations(), str->Declaration());
+                    ctx.Remove(src->AST().GlobalDeclarations(), str->Declaration());
                 }
             }
         }
@@ -119,11 +130,10 @@
     const ast::Variable* num_workgroups_ubo = nullptr;
     auto get_ubo = [&]() {
         if (!num_workgroups_ubo) {
-            auto* num_workgroups_struct = ctx.dst->Structure(
-                ctx.dst->Sym(),
-                utils::Vector{
-                    ctx.dst->Member(kNumWorkgroupsMemberName, ctx.dst->ty.vec3(ctx.dst->ty.u32())),
-                });
+            auto* num_workgroups_struct =
+                b.Structure(b.Sym(), utils::Vector{
+                                         b.Member(kNumWorkgroupsMemberName, b.ty.vec3(b.ty.u32())),
+                                     });
 
             uint32_t group, binding;
             if (cfg->ubo_binding.has_value()) {
@@ -135,9 +145,9 @@
                 // plus 1, or group 0 if no resource bound.
                 group = 0;
 
-                for (auto* global : ctx.src->AST().GlobalVariables()) {
+                for (auto* global : src->AST().GlobalVariables()) {
                     if (global->HasBindingPoint()) {
-                        auto* global_sem = ctx.src->Sem().Get<sem::GlobalVariable>(global);
+                        auto* global_sem = src->Sem().Get<sem::GlobalVariable>(global);
                         auto binding_point = global_sem->BindingPoint();
                         if (binding_point.group >= group) {
                             group = binding_point.group + 1;
@@ -148,16 +158,16 @@
                 binding = 0;
             }
 
-            num_workgroups_ubo = ctx.dst->GlobalVar(
-                ctx.dst->Sym(), ctx.dst->ty.Of(num_workgroups_struct), ast::AddressSpace::kUniform,
-                ctx.dst->Group(AInt(group)), ctx.dst->Binding(AInt(binding)));
+            num_workgroups_ubo =
+                b.GlobalVar(b.Sym(), b.ty.Of(num_workgroups_struct), ast::AddressSpace::kUniform,
+                            b.Group(AInt(group)), b.Binding(AInt(binding)));
         }
         return num_workgroups_ubo;
     };
 
     // Now replace all the places where the builtins are accessed with the value
     // loaded from the uniform buffer.
-    for (auto* node : ctx.src->ASTNodes().Objects()) {
+    for (auto* node : src->ASTNodes().Objects()) {
         auto* accessor = node->As<ast::MemberAccessorExpression>();
         if (!accessor) {
             continue;
@@ -168,12 +178,12 @@
         }
 
         if (to_replace.count({ident->symbol, accessor->member->symbol})) {
-            ctx.Replace(accessor,
-                        ctx.dst->MemberAccessor(get_ubo()->symbol, kNumWorkgroupsMemberName));
+            ctx.Replace(accessor, b.MemberAccessor(get_ubo()->symbol, kNumWorkgroupsMemberName));
         }
     }
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 NumWorkgroupsFromUniform::Config::Config(std::optional<sem::BindingPoint> ubo_bp)
diff --git a/src/tint/transform/num_workgroups_from_uniform.h b/src/tint/transform/num_workgroups_from_uniform.h
index 292c823..25308f2 100644
--- a/src/tint/transform/num_workgroups_from_uniform.h
+++ b/src/tint/transform/num_workgroups_from_uniform.h
@@ -72,19 +72,10 @@
         std::optional<sem::BindingPoint> ubo_binding;
     };
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/num_workgroups_from_uniform_test.cc b/src/tint/transform/num_workgroups_from_uniform_test.cc
index 093081c..435ab33 100644
--- a/src/tint/transform/num_workgroups_from_uniform_test.cc
+++ b/src/tint/transform/num_workgroups_from_uniform_test.cc
@@ -28,7 +28,9 @@
 TEST_F(NumWorkgroupsFromUniformTest, ShouldRunEmptyModule) {
     auto* src = R"()";
 
-    EXPECT_FALSE(ShouldRun<NumWorkgroupsFromUniform>(src));
+    DataMap data;
+    data.Add<NumWorkgroupsFromUniform::Config>(sem::BindingPoint{0, 30u});
+    EXPECT_FALSE(ShouldRun<NumWorkgroupsFromUniform>(src, data));
 }
 
 TEST_F(NumWorkgroupsFromUniformTest, ShouldRunHasNumWorkgroups) {
@@ -38,7 +40,9 @@
 }
 )";
 
-    EXPECT_TRUE(ShouldRun<NumWorkgroupsFromUniform>(src));
+    DataMap data;
+    data.Add<NumWorkgroupsFromUniform::Config>(sem::BindingPoint{0, 30u});
+    EXPECT_TRUE(ShouldRun<NumWorkgroupsFromUniform>(src, data));
 }
 
 TEST_F(NumWorkgroupsFromUniformTest, Error_MissingTransformData) {
@@ -55,7 +59,6 @@
     DataMap data;
     data.Add<CanonicalizeEntryPointIO::Config>(CanonicalizeEntryPointIO::ShaderStyle::kHlsl);
     auto got = Run<Unshadow, CanonicalizeEntryPointIO, NumWorkgroupsFromUniform>(src, data);
-
     EXPECT_EQ(expect, str(got));
 }
 
diff --git a/src/tint/transform/packed_vec3.cc b/src/tint/transform/packed_vec3.cc
index dde5aca..e947a53 100644
--- a/src/tint/transform/packed_vec3.cc
+++ b/src/tint/transform/packed_vec3.cc
@@ -33,14 +33,15 @@
 
 namespace tint::transform {
 
-/// The PIMPL state for the PackedVec3 transform
+/// PIMPL state for the transform
 struct PackedVec3::State {
     /// Constructor
-    /// @param c the CloneContext
-    explicit State(CloneContext& c) : ctx(c) {}
+    /// @param program the source program
+    explicit State(const Program* program) : src(program) {}
 
     /// Runs the transform
-    void Run() {
+    /// @returns the new program or SkipTransform if the transform is not required
+    ApplyResult Run() {
         // Packed vec3<T> struct members
         utils::Hashset<const sem::StructMember*, 8> members;
 
@@ -72,6 +73,10 @@
             }
         }
 
+        if (members.IsEmpty()) {
+            return SkipTransform;
+        }
+
         // Walk the nodes, starting with the most deeply nested, finding all the AST expressions
         // that load a whole packed vector (not a scalar / swizzle of the vector).
         utils::Hashset<const sem::Expression*, 16> refs;
@@ -137,36 +142,20 @@
         }
 
         ctx.Clone();
-    }
-
-    /// @returns true if this transform should be run for the given program
-    /// @param program the program to inspect
-    static bool ShouldRun(const Program* program) {
-        for (auto* decl : program->AST().GlobalDeclarations()) {
-            if (auto* str = program->Sem().Get<sem::Struct>(decl)) {
-                if (str->IsHostShareable()) {
-                    for (auto* member : str->Members()) {
-                        if (auto* vec = member->Type()->As<sem::Vector>()) {
-                            if (vec->Width() == 3) {
-                                return true;
-                            }
-                        }
-                    }
-                }
-            }
-        }
-        return false;
+        return Program(std::move(b));
     }
 
   private:
+    /// The source program
+    const Program* const src;
+    /// The target program builder
+    ProgramBuilder b;
     /// The clone context
-    CloneContext& ctx;
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
     /// Alias to the semantic info in ctx.src
     const sem::Info& sem = ctx.src->Sem();
     /// Alias to the symbols in ctx.src
     const SymbolTable& sym = ctx.src->Symbols();
-    /// Alias to the ctx.dst program builder
-    ProgramBuilder& b = *ctx.dst;
 };
 
 PackedVec3::Attribute::Attribute(ProgramID pid, ast::NodeID nid) : Base(pid, nid) {}
@@ -183,12 +172,8 @@
 PackedVec3::PackedVec3() = default;
 PackedVec3::~PackedVec3() = default;
 
-bool PackedVec3::ShouldRun(const Program* program, const DataMap&) const {
-    return State::ShouldRun(program);
-}
-
-void PackedVec3::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    State(ctx).Run();
+Transform::ApplyResult PackedVec3::Apply(const Program* src, const DataMap&, DataMap&) const {
+    return State{src}.Run();
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/packed_vec3.h b/src/tint/transform/packed_vec3.h
index 9d899cb..0d304fa 100644
--- a/src/tint/transform/packed_vec3.h
+++ b/src/tint/transform/packed_vec3.h
@@ -56,21 +56,13 @@
     /// Destructor
     ~PackedVec3() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
   private:
     struct State;
-
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/pad_structs.cc b/src/tint/transform/pad_structs.cc
index 10b0565..4ceb39d 100644
--- a/src/tint/transform/pad_structs.cc
+++ b/src/tint/transform/pad_structs.cc
@@ -50,8 +50,10 @@
 
 PadStructs::~PadStructs() = default;
 
-void PadStructs::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    auto& sem = ctx.src->Sem();
+Transform::ApplyResult PadStructs::Apply(const Program* src, const DataMap&, DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+    auto& sem = src->Sem();
 
     std::unordered_map<const ast::Struct*, const ast::Struct*> replaced_structs;
     utils::Hashset<const ast::StructMember*, 8> padding_members;
@@ -65,7 +67,7 @@
         bool has_runtime_sized_array = false;
         utils::Vector<const ast::StructMember*, 8> new_members;
         for (auto* mem : str->Members()) {
-            auto name = ctx.src->Symbols().NameFor(mem->Name());
+            auto name = src->Symbols().NameFor(mem->Name());
 
             if (offset < mem->Offset()) {
                 CreatePadding(&new_members, &padding_members, ctx.dst, mem->Offset() - offset);
@@ -75,7 +77,7 @@
             auto* ty = mem->Type();
             const ast::Type* type = CreateASTTypeFor(ctx, ty);
 
-            new_members.Push(ctx.dst->Member(name, type));
+            new_members.Push(b.Member(name, type));
 
             uint32_t size = ty->Size();
             if (ty->Is<sem::Struct>() && str->UsedAs(ast::AddressSpace::kUniform)) {
@@ -97,8 +99,8 @@
         if (offset < struct_size && !has_runtime_sized_array) {
             CreatePadding(&new_members, &padding_members, ctx.dst, struct_size - offset);
         }
-        auto* new_struct = ctx.dst->create<ast::Struct>(ctx.Clone(ast_str->name),
-                                                        std::move(new_members), utils::Empty);
+        auto* new_struct =
+            b.create<ast::Struct>(ctx.Clone(ast_str->name), std::move(new_members), utils::Empty);
         replaced_structs[ast_str] = new_struct;
         return new_struct;
     });
@@ -131,16 +133,17 @@
         auto* arg = ast_call->args.begin();
         for (auto* member : new_struct->members) {
             if (padding_members.Contains(member)) {
-                new_args.Push(ctx.dst->Expr(0_u));
+                new_args.Push(b.Expr(0_u));
             } else {
                 new_args.Push(ctx.Clone(*arg));
                 arg++;
             }
         }
-        return ctx.dst->Construct(CreateASTTypeFor(ctx, str), new_args);
+        return b.Construct(CreateASTTypeFor(ctx, str), new_args);
     });
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/pad_structs.h b/src/tint/transform/pad_structs.h
index 55fec74..e9996d4 100644
--- a/src/tint/transform/pad_structs.h
+++ b/src/tint/transform/pad_structs.h
@@ -30,14 +30,10 @@
     /// Destructor
     ~PadStructs() override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/promote_initializers_to_let.cc b/src/tint/transform/promote_initializers_to_let.cc
index 315a4ce..9e02c45 100644
--- a/src/tint/transform/promote_initializers_to_let.cc
+++ b/src/tint/transform/promote_initializers_to_let.cc
@@ -13,6 +13,9 @@
 // limitations under the License.
 
 #include "src/tint/transform/promote_initializers_to_let.h"
+
+#include <utility>
+
 #include "src/tint/program_builder.h"
 #include "src/tint/sem/call.h"
 #include "src/tint/sem/statement.h"
@@ -27,9 +30,16 @@
 
 PromoteInitializersToLet::~PromoteInitializersToLet() = default;
 
-void PromoteInitializersToLet::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+Transform::ApplyResult PromoteInitializersToLet::Apply(const Program* src,
+                                                       const DataMap&,
+                                                       DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     HoistToDeclBefore hoist_to_decl_before(ctx);
 
+    bool any_promoted = false;
+
     // Hoists array and structure initializers to a constant variable, declared
     // just before the statement of usage.
     auto promote = [&](const sem::Expression* expr) {
@@ -59,14 +69,15 @@
             return true;
         }
 
+        any_promoted = true;
         return hoist_to_decl_before.Add(expr, expr->Declaration(), true);
     };
 
-    for (auto* node : ctx.src->ASTNodes().Objects()) {
+    for (auto* node : src->ASTNodes().Objects()) {
         bool ok = Switch(
             node,  //
             [&](const ast::CallExpression* expr) {
-                if (auto* sem = ctx.src->Sem().Get(expr)) {
+                if (auto* sem = src->Sem().Get(expr)) {
                     auto* ctor = sem->UnwrapMaterialize()->As<sem::Call>();
                     if (ctor->Target()->Is<sem::TypeInitializer>()) {
                         return promote(sem);
@@ -75,7 +86,7 @@
                 return true;
             },
             [&](const ast::IdentifierExpression* expr) {
-                if (auto* sem = ctx.src->Sem().Get(expr)) {
+                if (auto* sem = src->Sem().Get(expr)) {
                     if (auto* user = sem->UnwrapMaterialize()->As<sem::VariableUser>()) {
                         // Identifier resolves to a variable
                         if (auto* stmt = user->Stmt()) {
@@ -96,13 +107,17 @@
                 return true;
             },
             [&](Default) { return true; });
-
         if (!ok) {
-            return;
+            return Program(std::move(b));
         }
     }
 
+    if (!any_promoted) {
+        return SkipTransform;
+    }
+
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/promote_initializers_to_let.h b/src/tint/transform/promote_initializers_to_let.h
index 78793c7..b1bb291 100644
--- a/src/tint/transform/promote_initializers_to_let.h
+++ b/src/tint/transform/promote_initializers_to_let.h
@@ -33,14 +33,10 @@
     /// Destructor
     ~PromoteInitializersToLet() override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/promote_side_effects_to_decl.cc b/src/tint/transform/promote_side_effects_to_decl.cc
index 2bcda04..ea13b0b 100644
--- a/src/tint/transform/promote_side_effects_to_decl.cc
+++ b/src/tint/transform/promote_side_effects_to_decl.cc
@@ -53,34 +53,36 @@
 // to else {if}s so that the next transform, DecomposeSideEffects, can insert
 // hoisted expressions above their current location.
 struct SimplifySideEffectStatements : Castable<PromoteSideEffectsToDecl, Transform> {
-    class State;
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap&) const override;
+    ApplyResult Apply(const Program* src, const DataMap& inputs, DataMap& outputs) const override;
 };
 
-class SimplifySideEffectStatements::State : public StateBase {
-    HoistToDeclBefore hoist_to_decl_before;
+Transform::ApplyResult SimplifySideEffectStatements::Apply(const Program* src,
+                                                           const DataMap&,
+                                                           DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
 
-  public:
-    explicit State(CloneContext& ctx_in) : StateBase(ctx_in), hoist_to_decl_before(ctx_in) {}
+    bool made_changes = false;
 
-    void Run() {
-        for (auto* node : ctx.src->ASTNodes().Objects()) {
-            if (auto* expr = node->As<ast::Expression>()) {
-                auto* sem_expr = sem.Get(expr);
-                if (!sem_expr || !sem_expr->HasSideEffects()) {
-                    continue;
-                }
-
-                hoist_to_decl_before.Prepare(sem_expr);
+    HoistToDeclBefore hoist_to_decl_before(ctx);
+    for (auto* node : ctx.src->ASTNodes().Objects()) {
+        if (auto* expr = node->As<ast::Expression>()) {
+            auto* sem_expr = src->Sem().Get(expr);
+            if (!sem_expr || !sem_expr->HasSideEffects()) {
+                continue;
             }
-        }
-        ctx.Clone();
-    }
-};
 
-void SimplifySideEffectStatements::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    State state(ctx);
-    state.Run();
+            hoist_to_decl_before.Prepare(sem_expr);
+            made_changes = true;
+        }
+    }
+
+    if (!made_changes) {
+        return SkipTransform;
+    }
+
+    ctx.Clone();
+    return Program(std::move(b));
 }
 
 // Decomposes side-effecting expressions to ensure order of evaluation. This
@@ -89,7 +91,7 @@
 struct DecomposeSideEffects : Castable<PromoteSideEffectsToDecl, Transform> {
     class CollectHoistsState;
     class DecomposeState;
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap&) const override;
+    ApplyResult Apply(const Program* src, const DataMap& inputs, DataMap& outputs) const override;
 };
 
 // CollectHoistsState traverses the AST top-down, identifying which expressions
@@ -667,12 +669,15 @@
             }
             return nullptr;
         });
-
-        ctx.Clone();
     }
 };
 
-void DecomposeSideEffects::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+Transform::ApplyResult DecomposeSideEffects::Apply(const Program* src,
+                                                   const DataMap&,
+                                                   DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     // First collect side-effecting expressions to hoist
     CollectHoistsState collect_hoists_state{ctx};
     auto to_hoist = collect_hoists_state.Run();
@@ -680,6 +685,9 @@
     // Now decompose these expressions
     DecomposeState decompose_state{ctx, std::move(to_hoist)};
     decompose_state.Run();
+
+    ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace
@@ -687,13 +695,13 @@
 PromoteSideEffectsToDecl::PromoteSideEffectsToDecl() = default;
 PromoteSideEffectsToDecl::~PromoteSideEffectsToDecl() = default;
 
-Output PromoteSideEffectsToDecl::Run(const Program* program, const DataMap& data) const {
+Transform::ApplyResult PromoteSideEffectsToDecl::Apply(const Program* src,
+                                                       const DataMap& inputs,
+                                                       DataMap& outputs) const {
     transform::Manager manager;
     manager.Add<SimplifySideEffectStatements>();
     manager.Add<DecomposeSideEffects>();
-
-    auto output = manager.Run(program, data);
-    return output;
+    return manager.Apply(src, inputs, outputs);
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/promote_side_effects_to_decl.h b/src/tint/transform/promote_side_effects_to_decl.h
index d5d1126..99e80c6 100644
--- a/src/tint/transform/promote_side_effects_to_decl.h
+++ b/src/tint/transform/promote_side_effects_to_decl.h
@@ -31,12 +31,10 @@
     /// Destructor
     ~PromoteSideEffectsToDecl() override;
 
-  protected:
-    /// Runs the transform on `program`, returning the transformation result.
-    /// @param program the source program to transform
-    /// @param data optional extra transform-specific data
-    /// @returns the transformation result
-    Output Run(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/remove_continue_in_switch.cc b/src/tint/transform/remove_continue_in_switch.cc
index e5df23f..cf0158f 100644
--- a/src/tint/transform/remove_continue_in_switch.cc
+++ b/src/tint/transform/remove_continue_in_switch.cc
@@ -32,53 +32,19 @@
 TINT_INSTANTIATE_TYPEINFO(tint::transform::RemoveContinueInSwitch);
 
 namespace tint::transform {
-namespace {
 
-class State {
-  private:
-    CloneContext& ctx;
-    ProgramBuilder& b;
-    const sem::Info& sem;
-
-    // Map of switch statement to 'tint_continue' variable.
-    std::unordered_map<const ast::SwitchStatement*, Symbol> switch_to_cont_var_name;
-
-    // If `cont` is within a switch statement within a loop, returns a pointer to
-    // that switch statement.
-    static const ast::SwitchStatement* GetParentSwitchInLoop(const sem::Info& sem,
-                                                             const ast::ContinueStatement* cont) {
-        // Find whether first parent is a switch or a loop
-        auto* sem_stmt = sem.Get(cont);
-        auto* sem_parent = sem_stmt->FindFirstParent<sem::SwitchStatement, sem::LoopBlockStatement,
-                                                     sem::ForLoopStatement, sem::WhileStatement>();
-        if (!sem_parent) {
-            return nullptr;
-        }
-        return sem_parent->Declaration()->As<ast::SwitchStatement>();
-    }
-
-  public:
+/// PIMPL state for the transform
+struct RemoveContinueInSwitch::State {
     /// Constructor
-    /// @param ctx_in the context
-    explicit State(CloneContext& ctx_in) : ctx(ctx_in), b(*ctx_in.dst), sem(ctx_in.src->Sem()) {}
-
-    /// Returns true if this transform should be run for the given program
-    static bool ShouldRun(const Program* program) {
-        for (auto* node : program->ASTNodes().Objects()) {
-            auto* stmt = node->As<ast::ContinueStatement>();
-            if (!stmt) {
-                continue;
-            }
-            if (GetParentSwitchInLoop(program->Sem(), stmt)) {
-                return true;
-            }
-        }
-        return false;
-    }
+    /// @param program the source program
+    explicit State(const Program* program) : src(program) {}
 
     /// Runs the transform
-    void Run() {
-        for (auto* node : ctx.src->ASTNodes().Objects()) {
+    /// @returns the new program or SkipTransform if the transform is not required
+    ApplyResult Run() {
+        bool made_changes = false;
+
+        for (auto* node : src->ASTNodes().Objects()) {
             auto* cont = node->As<ast::ContinueStatement>();
             if (!cont) {
                 continue;
@@ -90,6 +56,8 @@
                 continue;
             }
 
+            made_changes = true;
+
             auto cont_var_name =
                 tint::utils::GetOrCreate(switch_to_cont_var_name, switch_stmt, [&]() {
                     // Create and insert 'var tint_continue : bool = false;' before the
@@ -116,22 +84,50 @@
             ctx.Replace(cont, new_stmt);
         }
 
+        if (!made_changes) {
+            return SkipTransform;
+        }
+
         ctx.Clone();
+        return Program(std::move(b));
+    }
+
+  private:
+    /// The source program
+    const Program* const src;
+    /// The target program builder
+    ProgramBuilder b;
+    /// The clone context
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
+    /// Alias to src->sem
+    const sem::Info& sem = src->Sem();
+
+    // Map of switch statement to 'tint_continue' variable.
+    std::unordered_map<const ast::SwitchStatement*, Symbol> switch_to_cont_var_name;
+
+    // If `cont` is within a switch statement within a loop, returns a pointer to
+    // that switch statement.
+    static const ast::SwitchStatement* GetParentSwitchInLoop(const sem::Info& sem,
+                                                             const ast::ContinueStatement* cont) {
+        // Find whether first parent is a switch or a loop
+        auto* sem_stmt = sem.Get(cont);
+        auto* sem_parent = sem_stmt->FindFirstParent<sem::SwitchStatement, sem::LoopBlockStatement,
+                                                     sem::ForLoopStatement, sem::WhileStatement>();
+        if (!sem_parent) {
+            return nullptr;
+        }
+        return sem_parent->Declaration()->As<ast::SwitchStatement>();
     }
 };
 
-}  // namespace
-
 RemoveContinueInSwitch::RemoveContinueInSwitch() = default;
 RemoveContinueInSwitch::~RemoveContinueInSwitch() = default;
 
-bool RemoveContinueInSwitch::ShouldRun(const Program* program, const DataMap& /*data*/) const {
-    return State::ShouldRun(program);
-}
-
-void RemoveContinueInSwitch::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    State state(ctx);
-    state.Run();
+Transform::ApplyResult RemoveContinueInSwitch::Apply(const Program* src,
+                                                     const DataMap&,
+                                                     DataMap&) const {
+    State state(src);
+    return state.Run();
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/remove_continue_in_switch.h b/src/tint/transform/remove_continue_in_switch.h
index 9e5a4d5..1070906 100644
--- a/src/tint/transform/remove_continue_in_switch.h
+++ b/src/tint/transform/remove_continue_in_switch.h
@@ -31,19 +31,13 @@
     /// Destructor
     ~RemoveContinueInSwitch() override;
 
-  protected:
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+  private:
+    struct State;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/remove_phonies.cc b/src/tint/transform/remove_phonies.cc
index 1f84538..080152c 100644
--- a/src/tint/transform/remove_phonies.cc
+++ b/src/tint/transform/remove_phonies.cc
@@ -41,34 +41,25 @@
 
 RemovePhonies::~RemovePhonies() = default;
 
-bool RemovePhonies::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* node : program->ASTNodes().Objects()) {
-        if (node->Is<ast::PhonyExpression>()) {
-            return true;
-        }
-        if (auto* stmt = node->As<ast::CallStatement>()) {
-            if (program->Sem().Get(stmt->expr)->ConstantValue() != nullptr) {
-                return true;
-            }
-        }
-    }
-    return false;
-}
+Transform::ApplyResult RemovePhonies::Apply(const Program* src, const DataMap&, DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
 
-void RemovePhonies::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    auto& sem = ctx.src->Sem();
+    auto& sem = src->Sem();
 
-    std::unordered_map<SinkSignature, Symbol, utils::Hasher<SinkSignature>> sinks;
+    utils::Hashmap<SinkSignature, Symbol, 8, utils::Hasher<SinkSignature>> sinks;
 
-    for (auto* node : ctx.src->ASTNodes().Objects()) {
+    bool made_changes = false;
+    for (auto* node : src->ASTNodes().Objects()) {
         Switch(
             node,
             [&](const ast::AssignmentStatement* stmt) {
                 if (stmt->lhs->Is<ast::PhonyExpression>()) {
+                    made_changes = true;
+
                     std::vector<const ast::Expression*> side_effects;
                     if (!ast::TraverseExpressions(
-                            stmt->rhs, ctx.dst->Diagnostics(),
-                            [&](const ast::CallExpression* expr) {
+                            stmt->rhs, b.Diagnostics(), [&](const ast::CallExpression* expr) {
                                 // ast::CallExpression may map to a function or builtin call
                                 // (both may have side-effects), or a type initializer or
                                 // type conversion (both do not have side effects).
@@ -100,8 +91,7 @@
                         if (auto* call = side_effects[0]->As<ast::CallExpression>()) {
                             // Phony assignment with single call side effect.
                             // Replace phony assignment with call.
-                            ctx.Replace(stmt,
-                                        [&, call] { return ctx.dst->CallStmt(ctx.Clone(call)); });
+                            ctx.Replace(stmt, [&, call] { return b.CallStmt(ctx.Clone(call)); });
                             return;
                         }
                     }
@@ -114,22 +104,21 @@
                         for (auto* arg : side_effects) {
                             sig.push_back(sem.Get(arg)->Type()->UnwrapRef());
                         }
-                        auto sink = utils::GetOrCreate(sinks, sig, [&] {
-                            auto name = ctx.dst->Symbols().New("phony_sink");
+                        auto sink = sinks.GetOrCreate(sig, [&] {
+                            auto name = b.Symbols().New("phony_sink");
                             utils::Vector<const ast::Parameter*, 8> params;
                             for (auto* ty : sig) {
                                 auto* ast_ty = CreateASTTypeFor(ctx, ty);
-                                params.Push(
-                                    ctx.dst->Param("p" + std::to_string(params.Length()), ast_ty));
+                                params.Push(b.Param("p" + std::to_string(params.Length()), ast_ty));
                             }
-                            ctx.dst->Func(name, params, ctx.dst->ty.void_(), {});
+                            b.Func(name, params, b.ty.void_(), {});
                             return name;
                         });
                         utils::Vector<const ast::Expression*, 8> args;
                         for (auto* arg : side_effects) {
                             args.Push(ctx.Clone(arg));
                         }
-                        return ctx.dst->CallStmt(ctx.dst->Call(sink, args));
+                        return b.CallStmt(b.Call(sink, args));
                     });
                 }
             },
@@ -138,12 +127,18 @@
                 // TODO(crbug.com/tint/1637): Remove if `stmt->expr` has no side-effects.
                 auto* sem_expr = sem.Get(stmt->expr);
                 if ((sem_expr->ConstantValue() != nullptr) && !sem_expr->HasSideEffects()) {
+                    made_changes = true;
                     ctx.Remove(sem.Get(stmt)->Block()->Declaration()->statements, stmt);
                 }
             });
     }
 
+    if (!made_changes) {
+        return SkipTransform;
+    }
+
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/remove_phonies.h b/src/tint/transform/remove_phonies.h
index daa1812..99a049e 100644
--- a/src/tint/transform/remove_phonies.h
+++ b/src/tint/transform/remove_phonies.h
@@ -33,19 +33,10 @@
     /// Destructor
     ~RemovePhonies() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/remove_unreachable_statements.cc b/src/tint/transform/remove_unreachable_statements.cc
index 964d767..f9bf202 100644
--- a/src/tint/transform/remove_unreachable_statements.cc
+++ b/src/tint/transform/remove_unreachable_statements.cc
@@ -36,27 +36,28 @@
 
 RemoveUnreachableStatements::~RemoveUnreachableStatements() = default;
 
-bool RemoveUnreachableStatements::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* node : program->ASTNodes().Objects()) {
-        if (auto* stmt = program->Sem().Get<sem::Statement>(node)) {
+Transform::ApplyResult RemoveUnreachableStatements::Apply(const Program* src,
+                                                          const DataMap&,
+                                                          DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
+    bool made_changes = false;
+    for (auto* node : src->ASTNodes().Objects()) {
+        if (auto* stmt = src->Sem().Get<sem::Statement>(node)) {
             if (!stmt->IsReachable()) {
-                return true;
+                RemoveStatement(ctx, stmt->Declaration());
+                made_changes = true;
             }
         }
     }
-    return false;
-}
 
-void RemoveUnreachableStatements::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    for (auto* node : ctx.src->ASTNodes().Objects()) {
-        if (auto* stmt = ctx.src->Sem().Get<sem::Statement>(node)) {
-            if (!stmt->IsReachable()) {
-                RemoveStatement(ctx, stmt->Declaration());
-            }
-        }
+    if (!made_changes) {
+        return SkipTransform;
     }
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/remove_unreachable_statements.h b/src/tint/transform/remove_unreachable_statements.h
index 7f8b947..f5848f5 100644
--- a/src/tint/transform/remove_unreachable_statements.h
+++ b/src/tint/transform/remove_unreachable_statements.h
@@ -32,19 +32,10 @@
     /// Destructor
     ~RemoveUnreachableStatements() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/renamer.cc b/src/tint/transform/renamer.cc
index 562a52f..0fd1113 100644
--- a/src/tint/transform/renamer.cc
+++ b/src/tint/transform/renamer.cc
@@ -1252,39 +1252,31 @@
 Renamer::Renamer() = default;
 Renamer::~Renamer() = default;
 
-Output Renamer::Run(const Program* in, const DataMap& inputs) const {
-    ProgramBuilder out;
-    // Disable auto-cloning of symbols, since we want to rename them.
-    CloneContext ctx(&out, in, false);
+Transform::ApplyResult Renamer::Apply(const Program* src,
+                                      const DataMap& inputs,
+                                      DataMap& outputs) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ false};
 
     // Swizzles, builtin calls and builtin structure members need to keep their
     // symbols preserved.
-    std::unordered_set<const ast::IdentifierExpression*> preserve;
-    for (auto* node : in->ASTNodes().Objects()) {
+    utils::Hashset<const ast::IdentifierExpression*, 8> preserve;
+    for (auto* node : src->ASTNodes().Objects()) {
         if (auto* member = node->As<ast::MemberAccessorExpression>()) {
-            auto* sem = in->Sem().Get(member);
-            if (!sem) {
-                TINT_ICE(Transform, out.Diagnostics())
-                    << "MemberAccessorExpression has no semantic info";
-                continue;
-            }
+            auto* sem = src->Sem().Get(member);
             if (sem->Is<sem::Swizzle>()) {
-                preserve.emplace(member->member);
-            } else if (auto* str_expr = in->Sem().Get(member->structure)) {
+                preserve.Add(member->member);
+            } else if (auto* str_expr = src->Sem().Get(member->structure)) {
                 if (auto* ty = str_expr->Type()->UnwrapRef()->As<sem::Struct>()) {
                     if (ty->Declaration() == nullptr) {  // Builtin structure
-                        preserve.emplace(member->member);
+                        preserve.Add(member->member);
                     }
                 }
             }
         } else if (auto* call = node->As<ast::CallExpression>()) {
-            auto* sem = in->Sem().Get(call)->UnwrapMaterialize()->As<sem::Call>();
-            if (!sem) {
-                TINT_ICE(Transform, out.Diagnostics()) << "CallExpression has no semantic info";
-                continue;
-            }
+            auto* sem = src->Sem().Get(call)->UnwrapMaterialize()->As<sem::Call>();
             if (sem->Target()->Is<sem::Builtin>()) {
-                preserve.emplace(call->target.name);
+                preserve.Add(call->target.name);
             }
         }
     }
@@ -1300,7 +1292,7 @@
     }
 
     ctx.ReplaceAll([&](Symbol sym_in) {
-        auto name_in = ctx.src->Symbols().NameFor(sym_in);
+        auto name_in = src->Symbols().NameFor(sym_in);
         if (preserve_unicode || text::utf8::IsASCII(name_in)) {
             switch (target) {
                 case Target::kAll:
@@ -1343,17 +1335,20 @@
     });
 
     ctx.ReplaceAll([&](const ast::IdentifierExpression* ident) -> const ast::IdentifierExpression* {
-        if (preserve.count(ident)) {
+        if (preserve.Contains(ident)) {
             auto sym_in = ident->symbol;
-            auto str = in->Symbols().NameFor(sym_in);
-            auto sym_out = out.Symbols().Register(str);
+            auto str = src->Symbols().NameFor(sym_in);
+            auto sym_out = b.Symbols().Register(str);
             return ctx.dst->create<ast::IdentifierExpression>(ctx.Clone(ident->source), sym_out);
         }
         return nullptr;  // Clone ident. Uses the symbol remapping above.
     });
-    ctx.Clone();
 
-    return Output(Program(std::move(out)), std::make_unique<Data>(std::move(remappings)));
+    ctx.Clone();  // Must come before the std::move()
+
+    outputs.Add<Data>(std::move(remappings));
+
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/renamer.h b/src/tint/transform/renamer.h
index 000aee9..8a9f97e 100644
--- a/src/tint/transform/renamer.h
+++ b/src/tint/transform/renamer.h
@@ -85,11 +85,10 @@
     /// Destructor
     ~Renamer() override;
 
-    /// Runs the transform on `program`, returning the transformation result.
-    /// @param program the source program to transform
-    /// @param data optional extra transform-specific input data
-    /// @returns the transformation result
-    Output Run(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/robustness.cc b/src/tint/transform/robustness.cc
index a22f84f..75d63f2 100644
--- a/src/tint/transform/robustness.cc
+++ b/src/tint/transform/robustness.cc
@@ -33,36 +33,48 @@
 
 namespace tint::transform {
 
-/// State holds the current transform state
+/// PIMPL state for the transform
 struct Robustness::State {
-    /// The clone context
-    CloneContext& ctx;
+    /// Constructor
+    /// @param program the source program
+    /// @param omitted the omitted address spaces
+    State(const Program* program, std::unordered_set<ast::AddressSpace>&& omitted)
+        : src(program), omitted_address_spaces(std::move(omitted)) {}
 
-    /// Set of address spacees to not apply the transform to
-    std::unordered_set<ast::AddressSpace> omitted_classes;
-
-    /// Applies the transformation state to `ctx`.
-    void Transform() {
+    /// Runs the transform
+    /// @returns the new program or SkipTransform if the transform is not required
+    ApplyResult Run() {
         ctx.ReplaceAll([&](const ast::IndexAccessorExpression* expr) { return Transform(expr); });
         ctx.ReplaceAll([&](const ast::CallExpression* expr) { return Transform(expr); });
+
+        ctx.Clone();
+        return Program(std::move(b));
     }
 
+  private:
+    /// The source program
+    const Program* const src;
+    /// The target program builder
+    ProgramBuilder b;
+    /// The clone context
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
+
+    /// Set of address spaces to not apply the transform to
+    std::unordered_set<ast::AddressSpace> omitted_address_spaces;
+
     /// Apply bounds clamping to array, vector and matrix indexing
     /// @param expr the array, vector or matrix index expression
     /// @return the clamped replacement expression, or nullptr if `expr` should be cloned without
     /// changes.
     const ast::IndexAccessorExpression* Transform(const ast::IndexAccessorExpression* expr) {
-        auto* sem =
-            ctx.src->Sem().Get(expr)->UnwrapMaterialize()->As<sem::IndexAccessorExpression>();
+        auto* sem = src->Sem().Get(expr)->UnwrapMaterialize()->As<sem::IndexAccessorExpression>();
         auto* ret_type = sem->Type();
 
         auto* ref = ret_type->As<sem::Reference>();
-        if (ref && omitted_classes.count(ref->AddressSpace()) != 0) {
+        if (ref && omitted_address_spaces.count(ref->AddressSpace()) != 0) {
             return nullptr;
         }
 
-        ProgramBuilder& b = *ctx.dst;
-
         // idx return the cloned index expression, as a u32.
         auto idx = [&]() -> const ast::Expression* {
             auto* i = ctx.Clone(expr->index);
@@ -109,8 +121,8 @@
                 } else {
                     // Note: Don't be tempted to use the array override variable as an expression
                     // here, the name might be shadowed!
-                    ctx.dst->Diagnostics().add_error(diag::System::Transform,
-                                                     sem::Array::kErrExpectedConstantCount);
+                    b.Diagnostics().add_error(diag::System::Transform,
+                                              sem::Array::kErrExpectedConstantCount);
                     return nullptr;
                 }
 
@@ -119,7 +131,7 @@
             [&](Default) {
                 TINT_ICE(Transform, b.Diagnostics())
                     << "unhandled object type in robustness of array index: "
-                    << ctx.src->FriendlyName(ret_type->UnwrapRef());
+                    << src->FriendlyName(ret_type->UnwrapRef());
                 return nullptr;
             });
 
@@ -127,9 +139,9 @@
             return nullptr;  // Clamping not needed
         }
 
-        auto src = ctx.Clone(expr->source);
-        auto* obj = ctx.Clone(expr->object);
-        return b.IndexAccessor(src, obj, clamped_idx);
+        auto idx_src = ctx.Clone(expr->source);
+        auto* idx_obj = ctx.Clone(expr->object);
+        return b.IndexAccessor(idx_src, idx_obj, clamped_idx);
     }
 
     /// @param type builtin type
@@ -145,15 +157,13 @@
     /// @return the clamped replacement call expression, or nullptr if `expr`
     /// should be cloned without changes.
     const ast::CallExpression* Transform(const ast::CallExpression* expr) {
-        auto* call = ctx.src->Sem().Get(expr)->UnwrapMaterialize()->As<sem::Call>();
+        auto* call = src->Sem().Get(expr)->UnwrapMaterialize()->As<sem::Call>();
         auto* call_target = call->Target();
         auto* builtin = call_target->As<sem::Builtin>();
         if (!builtin || !TextureBuiltinNeedsClamping(builtin->Type())) {
             return nullptr;  // No transform, just clone.
         }
 
-        ProgramBuilder& b = *ctx.dst;
-
         // Indices of the mandatory texture and coords parameters, and the optional
         // array and level parameters.
         auto& signature = builtin->Signature();
@@ -261,7 +271,7 @@
         // Clamp the level argument, if provided
         if (level_idx >= 0) {
             auto* arg = expr->args[static_cast<size_t>(level_idx)];
-            ctx.Replace(arg, level_arg ? level_arg() : ctx.dst->Expr(0_a));
+            ctx.Replace(arg, level_arg ? level_arg() : b.Expr(0_a));
         }
 
         return nullptr;  // Clone, which will use the argument replacements above.
@@ -276,28 +286,27 @@
 Robustness::Robustness() = default;
 Robustness::~Robustness() = default;
 
-void Robustness::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) const {
+Transform::ApplyResult Robustness::Apply(const Program* src,
+                                         const DataMap& inputs,
+                                         DataMap&) const {
     Config cfg;
     if (auto* cfg_data = inputs.Get<Config>()) {
         cfg = *cfg_data;
     }
 
-    std::unordered_set<ast::AddressSpace> omitted_classes;
-    for (auto sc : cfg.omitted_classes) {
+    std::unordered_set<ast::AddressSpace> omitted_address_spaces;
+    for (auto sc : cfg.omitted_address_spaces) {
         switch (sc) {
             case AddressSpace::kUniform:
-                omitted_classes.insert(ast::AddressSpace::kUniform);
+                omitted_address_spaces.insert(ast::AddressSpace::kUniform);
                 break;
             case AddressSpace::kStorage:
-                omitted_classes.insert(ast::AddressSpace::kStorage);
+                omitted_address_spaces.insert(ast::AddressSpace::kStorage);
                 break;
         }
     }
 
-    State state{ctx, std::move(omitted_classes)};
-
-    state.Transform();
-    ctx.Clone();
+    return State{src, std::move(omitted_address_spaces)}.Run();
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/robustness.h b/src/tint/transform/robustness.h
index 21a7ff9..14c5fe1 100644
--- a/src/tint/transform/robustness.h
+++ b/src/tint/transform/robustness.h
@@ -54,9 +54,9 @@
         /// @returns this Config
         Config& operator=(const Config&);
 
-        /// Address spacees to omit from apply the transform to.
+        /// Address spaces to omit from apply the transform to.
         /// This allows for optimizing on hardware that provide safe accesses.
-        std::unordered_set<AddressSpace> omitted_classes;
+        std::unordered_set<AddressSpace> omitted_address_spaces;
     };
 
     /// Constructor
@@ -64,14 +64,10 @@
     /// Destructor
     ~Robustness() override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
   private:
     struct State;
diff --git a/src/tint/transform/robustness_test.cc b/src/tint/transform/robustness_test.cc
index 16d958f..990bbde 100644
--- a/src/tint/transform/robustness_test.cc
+++ b/src/tint/transform/robustness_test.cc
@@ -1274,7 +1274,7 @@
 )";
 
     Robustness::Config cfg;
-    cfg.omitted_classes.insert(Robustness::AddressSpace::kStorage);
+    cfg.omitted_address_spaces.insert(Robustness::AddressSpace::kStorage);
 
     DataMap data;
     data.Add<Robustness::Config>(cfg);
@@ -1325,7 +1325,7 @@
 )";
 
     Robustness::Config cfg;
-    cfg.omitted_classes.insert(Robustness::AddressSpace::kUniform);
+    cfg.omitted_address_spaces.insert(Robustness::AddressSpace::kUniform);
 
     DataMap data;
     data.Add<Robustness::Config>(cfg);
@@ -1376,8 +1376,8 @@
 )";
 
     Robustness::Config cfg;
-    cfg.omitted_classes.insert(Robustness::AddressSpace::kStorage);
-    cfg.omitted_classes.insert(Robustness::AddressSpace::kUniform);
+    cfg.omitted_address_spaces.insert(Robustness::AddressSpace::kStorage);
+    cfg.omitted_address_spaces.insert(Robustness::AddressSpace::kUniform);
 
     DataMap data;
     data.Add<Robustness::Config>(cfg);
diff --git a/src/tint/transform/simplify_pointers.cc b/src/tint/transform/simplify_pointers.cc
index ea35699..b2b99ed 100644
--- a/src/tint/transform/simplify_pointers.cc
+++ b/src/tint/transform/simplify_pointers.cc
@@ -45,14 +45,18 @@
 
 }  // namespace
 
-/// The PIMPL state for the SimplifyPointers transform
+/// PIMPL state for the transform
 struct SimplifyPointers::State {
+    /// The source program
+    const Program* const src;
+    /// The target program builder
+    ProgramBuilder b;
     /// The clone context
-    CloneContext& ctx;
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
 
     /// Constructor
-    /// @param context the clone context
-    explicit State(CloneContext& context) : ctx(context) {}
+    /// @param program the source program
+    explicit State(const Program* program) : src(program) {}
 
     /// Traverses the expression `expr` looking for non-literal array indexing
     /// expressions that would affect the computed address of a pointer
@@ -120,10 +124,11 @@
         }
     }
 
-    /// Performs the transformation
-    void Run() {
+    /// Runs the transform
+    /// @returns the new program or SkipTransform if the transform is not required
+    ApplyResult Run() {
         // A map of saved expressions to their saved variable name
-        std::unordered_map<const ast::Expression*, Symbol> saved_vars;
+        utils::Hashmap<const ast::Expression*, Symbol, 8> saved_vars;
 
         // Register the ast::Expression transform handler.
         // This performs two different transformations:
@@ -135,9 +140,8 @@
         // variable identifier.
         ctx.ReplaceAll([&](const ast::Expression* expr) -> const ast::Expression* {
             // Look to see if we need to swap this Expression with a saved variable.
-            auto it = saved_vars.find(expr);
-            if (it != saved_vars.end()) {
-                return ctx.dst->Expr(it->second);
+            if (auto* saved_var = saved_vars.Find(expr)) {
+                return ctx.dst->Expr(*saved_var);
             }
 
             // Reduce the expression, folding away chains of address-of / indirections
@@ -174,7 +178,7 @@
 
                 // Scan the initializer expression for array index expressions that need
                 // to be hoist to temporary "saved" variables.
-                std::vector<const ast::VariableDeclStatement*> saved;
+                utils::Vector<const ast::VariableDeclStatement*, 8> saved;
                 CollectSavedArrayIndices(
                     var->Declaration()->initializer, [&](const ast::Expression* idx_expr) {
                         // We have a sub-expression that needs to be saved.
@@ -182,18 +186,18 @@
                         auto saved_name = ctx.dst->Symbols().New(
                             ctx.src->Symbols().NameFor(var->Declaration()->symbol) + "_save");
                         auto* decl = ctx.dst->Decl(ctx.dst->Let(saved_name, ctx.Clone(idx_expr)));
-                        saved.emplace_back(decl);
+                        saved.Push(decl);
                         // Record the substitution of `idx_expr` to the saved variable
                         // with the symbol `saved_name`. This will be used by the
                         // ReplaceAll() handler above.
-                        saved_vars.emplace(idx_expr, saved_name);
+                        saved_vars.Add(idx_expr, saved_name);
                     });
 
                 // Find the place to insert the saved declarations.
                 // Special care needs to be made for lets declared as the initializer
                 // part of for-loops. In this case the block will hold the for-loop
                 // statement, not the let.
-                if (!saved.empty()) {
+                if (!saved.IsEmpty()) {
                     auto* stmt = ctx.src->Sem().Get(let);
                     auto* block = stmt->Block();
                     // Find the statement owned by the block (either the let decl or a
@@ -219,7 +223,9 @@
                 RemoveStatement(ctx, let);
             }
         }
+
         ctx.Clone();
+        return Program(std::move(b));
     }
 };
 
@@ -227,8 +233,8 @@
 
 SimplifyPointers::~SimplifyPointers() = default;
 
-void SimplifyPointers::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    State(ctx).Run();
+Transform::ApplyResult SimplifyPointers::Apply(const Program* src, const DataMap&, DataMap&) const {
+    return State(src).Run();
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/simplify_pointers.h b/src/tint/transform/simplify_pointers.h
index 787c7d8..6e040bb 100644
--- a/src/tint/transform/simplify_pointers.h
+++ b/src/tint/transform/simplify_pointers.h
@@ -39,16 +39,13 @@
     /// Destructor
     ~SimplifyPointers() override;
 
-  protected:
-    struct State;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+  private:
+    struct State;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/single_entry_point.cc b/src/tint/transform/single_entry_point.cc
index 8d26a7f..87787ae 100644
--- a/src/tint/transform/single_entry_point.cc
+++ b/src/tint/transform/single_entry_point.cc
@@ -30,33 +30,37 @@
 
 SingleEntryPoint::~SingleEntryPoint() = default;
 
-void SingleEntryPoint::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) const {
+Transform::ApplyResult SingleEntryPoint::Apply(const Program* src,
+                                               const DataMap& inputs,
+                                               DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     auto* cfg = inputs.Get<Config>();
     if (cfg == nullptr) {
-        ctx.dst->Diagnostics().add_error(
-            diag::System::Transform, "missing transform data for " + std::string(TypeInfo().name));
-
-        return;
+        b.Diagnostics().add_error(diag::System::Transform,
+                                  "missing transform data for " + std::string(TypeInfo().name));
+        return Program(std::move(b));
     }
 
     // Find the target entry point.
     const ast::Function* entry_point = nullptr;
-    for (auto* f : ctx.src->AST().Functions()) {
+    for (auto* f : src->AST().Functions()) {
         if (!f->IsEntryPoint()) {
             continue;
         }
-        if (ctx.src->Symbols().NameFor(f->symbol) == cfg->entry_point_name) {
+        if (src->Symbols().NameFor(f->symbol) == cfg->entry_point_name) {
             entry_point = f;
             break;
         }
     }
     if (entry_point == nullptr) {
-        ctx.dst->Diagnostics().add_error(diag::System::Transform,
-                                         "entry point '" + cfg->entry_point_name + "' not found");
-        return;
+        b.Diagnostics().add_error(diag::System::Transform,
+                                  "entry point '" + cfg->entry_point_name + "' not found");
+        return Program(std::move(b));
     }
 
-    auto& sem = ctx.src->Sem();
+    auto& sem = src->Sem();
 
     // Build set of referenced module-scope variables for faster lookups later.
     std::unordered_set<const ast::Variable*> referenced_vars;
@@ -66,12 +70,12 @@
 
     // Clone any module-scope variables, types, and functions that are statically referenced by the
     // target entry point.
-    for (auto* decl : ctx.src->AST().GlobalDeclarations()) {
+    for (auto* decl : src->AST().GlobalDeclarations()) {
         Switch(
             decl,  //
             [&](const ast::TypeDecl* ty) {
                 // TODO(jrprice): Strip unused types.
-                ctx.dst->AST().AddTypeDecl(ctx.Clone(ty));
+                b.AST().AddTypeDecl(ctx.Clone(ty));
             },
             [&](const ast::Override* override) {
                 if (referenced_vars.count(override)) {
@@ -80,37 +84,39 @@
                         // so that its allocated ID so that it won't be affected by other
                         // stripped away overrides
                         auto* global = sem.Get(override);
-                        const auto* id = ctx.dst->Id(global->OverrideId());
+                        const auto* id = b.Id(global->OverrideId());
                         ctx.InsertFront(override->attributes, id);
                     }
-                    ctx.dst->AST().AddGlobalVariable(ctx.Clone(override));
+                    b.AST().AddGlobalVariable(ctx.Clone(override));
                 }
             },
             [&](const ast::Var* var) {
                 if (referenced_vars.count(var)) {
-                    ctx.dst->AST().AddGlobalVariable(ctx.Clone(var));
+                    b.AST().AddGlobalVariable(ctx.Clone(var));
                 }
             },
             [&](const ast::Const* c) {
                 // Always keep 'const' declarations, as these can be used by attributes and array
                 // sizes, which are not tracked as transitively used by functions. They also don't
                 // typically get emitted by the backend unless they're actually used.
-                ctx.dst->AST().AddGlobalVariable(ctx.Clone(c));
+                b.AST().AddGlobalVariable(ctx.Clone(c));
             },
             [&](const ast::Function* func) {
                 if (sem.Get(func)->HasAncestorEntryPoint(entry_point->symbol)) {
-                    ctx.dst->AST().AddFunction(ctx.Clone(func));
+                    b.AST().AddFunction(ctx.Clone(func));
                 }
             },
-            [&](const ast::Enable* ext) { ctx.dst->AST().AddEnable(ctx.Clone(ext)); },
+            [&](const ast::Enable* ext) { b.AST().AddEnable(ctx.Clone(ext)); },
             [&](Default) {
-                TINT_UNREACHABLE(Transform, ctx.dst->Diagnostics())
+                TINT_UNREACHABLE(Transform, b.Diagnostics())
                     << "unhandled global declaration: " << decl->TypeInfo().name;
             });
     }
 
     // Clone the entry point.
-    ctx.dst->AST().AddFunction(ctx.Clone(entry_point));
+    b.AST().AddFunction(ctx.Clone(entry_point));
+
+    return Program(std::move(b));
 }
 
 SingleEntryPoint::Config::Config(std::string entry_point) : entry_point_name(entry_point) {}
diff --git a/src/tint/transform/single_entry_point.h b/src/tint/transform/single_entry_point.h
index 59aa021..7aba5e8 100644
--- a/src/tint/transform/single_entry_point.h
+++ b/src/tint/transform/single_entry_point.h
@@ -53,14 +53,10 @@
     /// Destructor
     ~SingleEntryPoint() override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/spirv_atomic.cc b/src/tint/transform/spirv_atomic.cc
index 127c702..eba6681 100644
--- a/src/tint/transform/spirv_atomic.cc
+++ b/src/tint/transform/spirv_atomic.cc
@@ -37,7 +37,7 @@
 
 using namespace tint::number_suffixes;  // NOLINT
 
-/// Private implementation of transform
+/// PIMPL state for the transform
 struct SpirvAtomic::State {
   private:
     /// A struct that has been forked because a subset of members were made atomic.
@@ -46,19 +46,24 @@
         std::unordered_set<size_t> atomic_members;
     };
 
-    CloneContext& ctx;
-    ProgramBuilder& b = *ctx.dst;
+    /// The source program
+    const Program* const src;
+    /// The target program builder
+    ProgramBuilder b;
+    /// The clone context
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
     std::unordered_map<const ast::Struct*, ForkedStruct> forked_structs;
     std::unordered_set<const sem::Variable*> atomic_variables;
     utils::UniqueVector<const sem::Expression*, 8> atomic_expressions;
 
   public:
     /// Constructor
-    /// @param c the clone context
-    explicit State(CloneContext& c) : ctx(c) {}
+    /// @param program the source program
+    explicit State(const Program* program) : src(program) {}
 
     /// Runs the transform
-    void Run() {
+    /// @returns the new program or SkipTransform if the transform is not required
+    ApplyResult Run() {
         // Look for stub functions generated by the SPIR-V reader, which are used as placeholders
         // for atomic builtin calls.
         for (auto* fn : ctx.src->AST().Functions()) {
@@ -102,6 +107,10 @@
             }
         }
 
+        if (atomic_expressions.IsEmpty()) {
+            return SkipTransform;
+        }
+
         // Transform all variables and structure members that were used in atomic operations as
         // atomic types. This propagates up originating expression chains.
         ProcessAtomicExpressions();
@@ -143,6 +152,7 @@
         ReplaceLoadsAndStores();
 
         ctx.Clone();
+        return Program(std::move(b));
     }
 
   private:
@@ -297,17 +307,8 @@
                                                           ctx->dst->AllocateNodeID(), builtin);
 }
 
-bool SpirvAtomic::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* fn : program->AST().Functions()) {
-        if (ast::HasAttribute<Stub>(fn->attributes)) {
-            return true;
-        }
-    }
-    return false;
-}
-
-void SpirvAtomic::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    State{ctx}.Run();
+Transform::ApplyResult SpirvAtomic::Apply(const Program* src, const DataMap&, DataMap&) const {
+    return State{src}.Run();
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/spirv_atomic.h b/src/tint/transform/spirv_atomic.h
index e1311c5..0f99dba 100644
--- a/src/tint/transform/spirv_atomic.h
+++ b/src/tint/transform/spirv_atomic.h
@@ -63,21 +63,13 @@
         const sem::BuiltinType builtin;
     };
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-  protected:
+  private:
     struct State;
-
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/std140.cc b/src/tint/transform/std140.cc
index 920fc69..0746bda 100644
--- a/src/tint/transform/std140.cc
+++ b/src/tint/transform/std140.cc
@@ -77,14 +77,20 @@
 
 namespace tint::transform {
 
-/// The PIMPL state for the Std140 transform
+/// PIMPL state for the transform
 struct Std140::State {
     /// Constructor
-    /// @param c the CloneContext
-    explicit State(CloneContext& c) : ctx(c) {}
+    /// @param program the source program
+    explicit State(const Program* program) : src(program) {}
 
     /// Runs the transform
-    void Run() {
+    /// @returns the new program or SkipTransform if the transform is not required
+    ApplyResult Run() {
+        if (!ShouldRun()) {
+            // Transform is not required
+            return SkipTransform;
+        }
+
         // Begin by creating forked types for any type that is used as a uniform buffer, that
         // either directly or transitively contains a matrix that needs splitting for std140 layout.
         ForkTypes();
@@ -116,11 +122,11 @@
         });
 
         ctx.Clone();
+        return Program(std::move(b));
     }
 
     /// @returns true if this transform should be run for the given program
-    /// @param program the program to inspect
-    static bool ShouldRun(const Program* program) {
+    bool ShouldRun() const {
         // Returns true if the type needs to be forked for std140 usage.
         auto needs_fork = [&](const sem::Type* ty) {
             while (auto* arr = ty->As<sem::Array>()) {
@@ -135,7 +141,7 @@
         };
 
         // Scan structures for members that need forking
-        for (auto* ty : program->Types()) {
+        for (auto* ty : src->Types()) {
             if (auto* str = ty->As<sem::Struct>()) {
                 if (str->UsedAs(ast::AddressSpace::kUniform)) {
                     for (auto* member : str->Members()) {
@@ -148,8 +154,8 @@
         }
 
         // Scan uniform variables that have types that need forking
-        for (auto* decl : program->AST().GlobalVariables()) {
-            auto* global = program->Sem().Get(decl);
+        for (auto* decl : src->AST().GlobalVariables()) {
+            auto* global = src->Sem().Get(decl);
             if (global->AddressSpace() == ast::AddressSpace::kUniform) {
                 if (needs_fork(global->Type()->UnwrapRef())) {
                     return true;
@@ -197,14 +203,16 @@
         }
     };
 
+    /// The source program
+    const Program* const src;
+    /// The target program builder
+    ProgramBuilder b;
     /// The clone context
-    CloneContext& ctx;
-    /// Alias to the semantic info in ctx.src
-    const sem::Info& sem = ctx.src->Sem();
-    /// Alias to the symbols in ctx.src
-    const SymbolTable& sym = ctx.src->Symbols();
-    /// Alias to the ctx.dst program builder
-    ProgramBuilder& b = *ctx.dst;
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
+    /// Alias to the semantic info in src
+    const sem::Info& sem = src->Sem();
+    /// Alias to the symbols in src
+    const SymbolTable& sym = src->Symbols();
 
     /// Map of load function signature, to the generated function
     utils::Hashmap<LoadFnKey, Symbol, 8, LoadFnKey::Hasher> load_fns;
@@ -218,7 +226,7 @@
     // Map of original structure to 'std140' forked structure
     utils::Hashmap<const sem::Struct*, Symbol, 8> std140_structs;
 
-    // Map of structure member in ctx.src of a matrix type, to list of decomposed column
+    // Map of structure member in src of a matrix type, to list of decomposed column
     // members in ctx.dst.
     utils::Hashmap<const sem::StructMember*, utils::Vector<const ast::StructMember*, 4>, 8>
         std140_mat_members;
@@ -232,7 +240,7 @@
         utils::Vector<Symbol, 4> columns;
     };
 
-    // Map of matrix type in ctx.src, to decomposed column structure in ctx.dst.
+    // Map of matrix type in src, to decomposed column structure in ctx.dst.
     utils::Hashmap<const sem::Matrix*, Std140Matrix, 8> std140_mats;
 
     /// AccessChain describes a chain of access expressions to uniform buffer variable.
@@ -266,7 +274,7 @@
     /// map (via Std140Type()).
     void ForkTypes() {
         // For each module scope declaration...
-        for (auto* global : ctx.src->Sem().Module()->DependencyOrderedDeclarations()) {
+        for (auto* global : src->Sem().Module()->DependencyOrderedDeclarations()) {
             // Check to see if this is a structure used by a uniform buffer...
             auto* str = sem.Get<sem::Struct>(global);
             if (str && str->UsedAs(ast::AddressSpace::kUniform)) {
@@ -317,7 +325,7 @@
                 if (fork_std140) {
                     // Clone any members that have not already been cloned.
                     for (auto& member : members) {
-                        if (member->program_id == ctx.src->ID()) {
+                        if (member->program_id == src->ID()) {
                             member = ctx.Clone(member);
                         }
                     }
@@ -326,7 +334,7 @@
                     auto name = b.Symbols().New(sym.NameFor(str->Name()) + "_std140");
                     auto* std140 = b.create<ast::Struct>(name, std::move(members),
                                                          ctx.Clone(str->Declaration()->attributes));
-                    ctx.InsertAfter(ctx.src->AST().GlobalDeclarations(), global, std140);
+                    ctx.InsertAfter(src->AST().GlobalDeclarations(), global, std140);
                     std140_structs.Add(str, name);
                 }
             }
@@ -337,14 +345,13 @@
     /// type that has been forked for std140-layout.
     /// Populates the #std140_uniforms set.
     void ReplaceUniformVarTypes() {
-        for (auto* global : ctx.src->AST().GlobalVariables()) {
+        for (auto* global : src->AST().GlobalVariables()) {
             if (auto* var = global->As<ast::Var>()) {
                 if (var->declared_address_space == ast::AddressSpace::kUniform) {
                     auto* v = sem.Get(var);
                     if (auto* std140_ty = Std140Type(v->Type()->UnwrapRef())) {
                         ctx.Replace(global->type, std140_ty);
                         std140_uniforms.Add(v);
-                        continue;
                     }
                 }
             }
@@ -404,7 +411,7 @@
                     auto std140_mat = std140_mats.GetOrCreate(mat, [&] {
                         auto name = b.Symbols().New("mat" + std::to_string(mat->columns()) + "x" +
                                                     std::to_string(mat->rows()) + "_" +
-                                                    ctx.src->FriendlyName(mat->type()));
+                                                    src->FriendlyName(mat->type()));
                         auto members =
                             DecomposedMatrixStructMembers(mat, "col", mat->Align(), mat->Size());
                         b.Structure(name, members);
@@ -421,7 +428,7 @@
                 if (auto* std140 = Std140Type(arr->ElemType())) {
                     utils::Vector<const ast::Attribute*, 1> attrs;
                     if (!arr->IsStrideImplicit()) {
-                        attrs.Push(ctx.dst->create<ast::StrideAttribute>(arr->Stride()));
+                        attrs.Push(b.create<ast::StrideAttribute>(arr->Stride()));
                     }
                     auto count = arr->ConstantCount();
                     if (!count) {
@@ -429,7 +436,7 @@
                         // * Override-expression counts can only be applied to workgroup arrays, and
                         //   this method only handles types transitively used as uniform buffers.
                         // * Runtime-sized arrays cannot be used in uniform buffers.
-                        TINT_ICE(Transform, ctx.dst->Diagnostics())
+                        TINT_ICE(Transform, b.Diagnostics())
                             << "unexpected non-constant array count";
                         count = 1;
                     }
@@ -440,7 +447,7 @@
             });
     }
 
-    /// @param mat the matrix to decompose (in ctx.src)
+    /// @param mat the matrix to decompose (in src)
     /// @param name_prefix the name prefix to apply to each of the returned column vector members.
     /// @param align the alignment in bytes of the matrix.
     /// @param size the size in bytes of the matrix.
@@ -473,7 +480,7 @@
             // Build the member
             const auto col_name = name_prefix + std::to_string(i);
             const auto* col_ty = CreateASTTypeFor(ctx, mat->ColumnType());
-            const auto* col_member = ctx.dst->Member(col_name, col_ty, std::move(attributes));
+            const auto* col_member = b.Member(col_name, col_ty, std::move(attributes));
             // Record the member for std140_mat_members
             out.Push(col_member);
         }
@@ -618,7 +625,7 @@
 
     /// @returns a name suffix for a std140 -> non-std140 conversion function based on the type
     ///          being converted.
-    const std::string ConvertSuffix(const sem::Type* ty) const {
+    const std::string ConvertSuffix(const sem::Type* ty) {
         return Switch(
             ty,  //
             [&](const sem::Struct* str) { return sym.NameFor(str->Name()); },
@@ -629,8 +636,7 @@
                     // * Override-expression counts can only be applied to workgroup arrays, and
                     //   this method only handles types transitively used as uniform buffers.
                     // * Runtime-sized arrays cannot be used in uniform buffers.
-                    TINT_ICE(Transform, ctx.dst->Diagnostics())
-                        << "unexpected non-constant array count";
+                    TINT_ICE(Transform, b.Diagnostics()) << "unexpected non-constant array count";
                     count = 1;
                 }
                 return "arr" + std::to_string(count.value()) + "_" + ConvertSuffix(arr->ElemType());
@@ -642,7 +648,7 @@
             [&](const sem::F32*) { return "f32"; },
             [&](Default) {
                 TINT_ICE(Transform, b.Diagnostics())
-                    << "unhandled type for conversion name: " << ctx.src->FriendlyName(ty);
+                    << "unhandled type for conversion name: " << src->FriendlyName(ty);
                 return "";
             });
     }
@@ -718,8 +724,7 @@
                         stmts.Push(b.Return(b.Construct(mat_ty, std::move(mat_args))));
                     } else {
                         TINT_ICE(Transform, b.Diagnostics())
-                            << "failed to find std140 matrix info for: "
-                            << ctx.src->FriendlyName(ty);
+                            << "failed to find std140 matrix info for: " << src->FriendlyName(ty);
                     }
                 },  //
                 [&](const sem::Array* arr) {
@@ -736,7 +741,7 @@
                         // * Override-expression counts can only be applied to workgroup arrays, and
                         //   this method only handles types transitively used as uniform buffers.
                         // * Runtime-sized arrays cannot be used in uniform buffers.
-                        TINT_ICE(Transform, ctx.dst->Diagnostics())
+                        TINT_ICE(Transform, b.Diagnostics())
                             << "unexpected non-constant array count";
                         count = 1;
                     }
@@ -749,7 +754,7 @@
                 },
                 [&](Default) {
                     TINT_ICE(Transform, b.Diagnostics())
-                        << "unhandled type for conversion: " << ctx.src->FriendlyName(ty);
+                        << "unhandled type for conversion: " << src->FriendlyName(ty);
                 });
 
             // Generate the function
@@ -1063,7 +1068,7 @@
 
         if (std::get_if<UniformVariable>(&access)) {
             const auto* expr = b.Expr(ctx.Clone(chain.var->Declaration()->symbol));
-            const auto name = ctx.src->Symbols().NameFor(chain.var->Declaration()->symbol);
+            const auto name = src->Symbols().NameFor(chain.var->Declaration()->symbol);
             ty = chain.var->Type()->UnwrapRef();
             return {expr, ty, name};
         }
@@ -1090,7 +1095,7 @@
                 },  //
                 [&](Default) -> ExprTypeName {
                     TINT_ICE(Transform, b.Diagnostics())
-                        << "unhandled type for access chain: " << ctx.src->FriendlyName(ty);
+                        << "unhandled type for access chain: " << src->FriendlyName(ty);
                     return {};
                 });
         }
@@ -1104,14 +1109,14 @@
                     for (auto el : *swizzle) {
                         rhs += xyzw[el];
                     }
-                    auto swizzle_ty = ctx.src->Types().Find<sem::Vector>(
+                    auto swizzle_ty = src->Types().Find<sem::Vector>(
                         vec->type(), static_cast<uint32_t>(swizzle->Length()));
                     auto* expr = b.MemberAccessor(lhs, rhs);
                     return {expr, swizzle_ty, rhs};
                 },  //
                 [&](Default) -> ExprTypeName {
                     TINT_ICE(Transform, b.Diagnostics())
-                        << "unhandled type for access chain: " << ctx.src->FriendlyName(ty);
+                        << "unhandled type for access chain: " << src->FriendlyName(ty);
                     return {};
                 });
         }
@@ -1140,7 +1145,7 @@
             },  //
             [&](Default) -> ExprTypeName {
                 TINT_ICE(Transform, b.Diagnostics())
-                    << "unhandled type for access chain: " << ctx.src->FriendlyName(ty);
+                    << "unhandled type for access chain: " << src->FriendlyName(ty);
                 return {};
             });
     }
@@ -1150,12 +1155,8 @@
 
 Std140::~Std140() = default;
 
-bool Std140::ShouldRun(const Program* program, const DataMap&) const {
-    return State::ShouldRun(program);
-}
-
-void Std140::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    State(ctx).Run();
+Transform::ApplyResult Std140::Apply(const Program* src, const DataMap&, DataMap&) const {
+    return State(src).Run();
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/std140.h b/src/tint/transform/std140.h
index ec5cad5..49e663d 100644
--- a/src/tint/transform/std140.h
+++ b/src/tint/transform/std140.h
@@ -34,21 +34,13 @@
     /// Destructor
     ~Std140() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
   private:
     struct State;
-
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/substitute_override.cc b/src/tint/transform/substitute_override.cc
index 2de04e0..7c2d0a2 100644
--- a/src/tint/transform/substitute_override.cc
+++ b/src/tint/transform/substitute_override.cc
@@ -15,6 +15,7 @@
 #include "src/tint/transform/substitute_override.h"
 
 #include <functional>
+#include <utility>
 
 #include "src/tint/program_builder.h"
 #include "src/tint/sem/builtin.h"
@@ -25,12 +26,9 @@
 TINT_INSTANTIATE_TYPEINFO(tint::transform::SubstituteOverride::Config);
 
 namespace tint::transform {
+namespace {
 
-SubstituteOverride::SubstituteOverride() = default;
-
-SubstituteOverride::~SubstituteOverride() = default;
-
-bool SubstituteOverride::ShouldRun(const Program* program, const DataMap&) const {
+bool ShouldRun(const Program* program) {
     for (auto* node : program->AST().GlobalVariables()) {
         if (node->Is<ast::Override>()) {
             return true;
@@ -39,18 +37,32 @@
     return false;
 }
 
-void SubstituteOverride::Run(CloneContext& ctx, const DataMap& config, DataMap&) const {
+}  // namespace
+
+SubstituteOverride::SubstituteOverride() = default;
+
+SubstituteOverride::~SubstituteOverride() = default;
+
+Transform::ApplyResult SubstituteOverride::Apply(const Program* src,
+                                                 const DataMap& config,
+                                                 DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     const auto* data = config.Get<Config>();
     if (!data) {
-        ctx.dst->Diagnostics().add_error(diag::System::Transform,
-                                         "Missing override substitution data");
-        return;
+        b.Diagnostics().add_error(diag::System::Transform, "Missing override substitution data");
+        return Program(std::move(b));
+    }
+
+    if (!ShouldRun(ctx.src)) {
+        return SkipTransform;
     }
 
     ctx.ReplaceAll([&](const ast::Override* w) -> const ast::Const* {
         auto* sem = ctx.src->Sem().Get(w);
 
-        auto src = ctx.Clone(w->source);
+        auto source = ctx.Clone(w->source);
         auto sym = ctx.Clone(w->symbol);
         auto* ty = ctx.Clone(w->type);
 
@@ -58,30 +70,30 @@
         auto iter = data->map.find(sem->OverrideId());
         if (iter == data->map.end()) {
             if (!w->initializer) {
-                ctx.dst->Diagnostics().add_error(
+                b.Diagnostics().add_error(
                     diag::System::Transform,
                     "Initializer not provided for override, and override not overridden.");
                 return nullptr;
             }
-            return ctx.dst->Const(src, sym, ty, ctx.Clone(w->initializer));
+            return b.Const(source, sym, ty, ctx.Clone(w->initializer));
         }
 
         auto value = iter->second;
         auto* ctor = Switch(
             sem->Type(),
-            [&](const sem::Bool*) { return ctx.dst->Expr(!std::equal_to<double>()(value, 0.0)); },
-            [&](const sem::I32*) { return ctx.dst->Expr(i32(value)); },
-            [&](const sem::U32*) { return ctx.dst->Expr(u32(value)); },
-            [&](const sem::F32*) { return ctx.dst->Expr(f32(value)); },
-            [&](const sem::F16*) { return ctx.dst->Expr(f16(value)); });
+            [&](const sem::Bool*) { return b.Expr(!std::equal_to<double>()(value, 0.0)); },
+            [&](const sem::I32*) { return b.Expr(i32(value)); },
+            [&](const sem::U32*) { return b.Expr(u32(value)); },
+            [&](const sem::F32*) { return b.Expr(f32(value)); },
+            [&](const sem::F16*) { return b.Expr(f16(value)); });
 
         if (!ctor) {
-            ctx.dst->Diagnostics().add_error(diag::System::Transform,
-                                             "Failed to create override-expression");
+            b.Diagnostics().add_error(diag::System::Transform,
+                                      "Failed to create override-expression");
             return nullptr;
         }
 
-        return ctx.dst->Const(src, sym, ty, ctor);
+        return b.Const(source, sym, ty, ctor);
     });
 
     // Ensure that objects that are indexed with an override-expression are materialized.
@@ -89,11 +101,10 @@
     // resulting type of the index may change. See: crbug.com/tint/1697.
     ctx.ReplaceAll(
         [&](const ast::IndexAccessorExpression* expr) -> const ast::IndexAccessorExpression* {
-            if (auto* sem = ctx.src->Sem().Get(expr)) {
+            if (auto* sem = src->Sem().Get(expr)) {
                 if (auto* access = sem->UnwrapMaterialize()->As<sem::IndexAccessorExpression>()) {
                     if (access->Object()->UnwrapMaterialize()->Type()->HoldsAbstract() &&
                         access->Index()->Stage() == sem::EvaluationStage::kOverride) {
-                        auto& b = *ctx.dst;
                         auto* obj = b.Call(sem::str(sem::BuiltinType::kTintMaterialize),
                                            ctx.Clone(expr->object));
                         return b.IndexAccessor(obj, ctx.Clone(expr->index));
@@ -104,6 +115,7 @@
         });
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 SubstituteOverride::Config::Config() = default;
diff --git a/src/tint/transform/substitute_override.h b/src/tint/transform/substitute_override.h
index 940e11d..853acc7 100644
--- a/src/tint/transform/substitute_override.h
+++ b/src/tint/transform/substitute_override.h
@@ -75,19 +75,10 @@
     /// Destructor
     ~SubstituteOverride() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/test_helper.h b/src/tint/transform/test_helper.h
index bc82fe5..ac48c5f 100644
--- a/src/tint/transform/test_helper.h
+++ b/src/tint/transform/test_helper.h
@@ -122,7 +122,18 @@
         }
 
         const Transform& t = TRANSFORM();
-        return t.ShouldRun(&program, data);
+
+        DataMap outputs;
+        auto result = t.Apply(&program, data, outputs);
+        if (!result) {
+            return false;
+        }
+        if (!result->IsValid()) {
+            ADD_FAILURE() << "Apply() called by ShouldRun() returned errors: "
+                          << result->Diagnostics().str();
+            return true;
+        }
+        return result.has_value();
     }
 
     /// @param in the input WGSL source
diff --git a/src/tint/transform/transform.cc b/src/tint/transform/transform.cc
index 3e03411..c37f3b4 100644
--- a/src/tint/transform/transform.cc
+++ b/src/tint/transform/transform.cc
@@ -46,24 +46,19 @@
 Transform::Transform() = default;
 Transform::~Transform() = default;
 
-Output Transform::Run(const Program* program, const DataMap& data /* = {} */) const {
-    ProgramBuilder builder;
-    CloneContext ctx(&builder, program);
+Output Transform::Run(const Program* src, const DataMap& data /* = {} */) const {
     Output output;
-    Run(ctx, data, output.data);
-    output.program = Program(std::move(builder));
+    if (auto program = Apply(src, data, output.data)) {
+        output.program = std::move(program.value());
+    } else {
+        ProgramBuilder b;
+        CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+        ctx.Clone();
+        output.program = Program(std::move(b));
+    }
     return output;
 }
 
-void Transform::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    TINT_UNIMPLEMENTED(Transform, ctx.dst->Diagnostics())
-        << "Transform::Run() unimplemented for " << TypeInfo().name;
-}
-
-bool Transform::ShouldRun(const Program*, const DataMap&) const {
-    return true;
-}
-
 void Transform::RemoveStatement(CloneContext& ctx, const ast::Statement* stmt) {
     auto* sem = ctx.src->Sem().Get(stmt);
     if (auto* block = tint::As<sem::BlockStatement>(sem->Parent())) {
diff --git a/src/tint/transform/transform.h b/src/tint/transform/transform.h
index c3e3d1d..6580e25 100644
--- a/src/tint/transform/transform.h
+++ b/src/tint/transform/transform.h
@@ -158,26 +158,30 @@
     /// Destructor
     ~Transform() override;
 
-    /// Runs the transform on `program`, returning the transformation result.
+    /// Runs the transform on @p program, returning the transformation result or a clone of
+    /// @p program.
     /// @param program the source program to transform
     /// @param data optional extra transform-specific input data
     /// @returns the transformation result
-    virtual Output Run(const Program* program, const DataMap& data = {}) const;
+    Output Run(const Program* program, const DataMap& data = {}) const;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    virtual bool ShouldRun(const Program* program, const DataMap& data = {}) const;
+    /// The return value of Apply().
+    /// If SkipTransform (std::nullopt), then the transform is not needed to be run.
+    using ApplyResult = std::optional<Program>;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
+    /// Value returned from Apply() to indicate that the transform does not need to be run
+    static inline constexpr std::nullopt_t SkipTransform = std::nullopt;
+
+    /// Runs the transform on `program`, return.
+    /// @param program the input program
     /// @param inputs optional extra transform-specific input data
     /// @param outputs optional extra transform-specific output data
-    virtual void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const;
+    /// @returns a transformed program, or std::nullopt if the transform didn't need to run.
+    virtual ApplyResult Apply(const Program* program,
+                              const DataMap& inputs,
+                              DataMap& outputs) const = 0;
 
+  protected:
     /// Removes the statement `stmt` from the transformed program.
     /// RemoveStatement handles edge cases, like statements in the initializer and
     /// continuing of for-loops.
diff --git a/src/tint/transform/transform_test.cc b/src/tint/transform/transform_test.cc
index d063ba2..82fdf6a 100644
--- a/src/tint/transform/transform_test.cc
+++ b/src/tint/transform/transform_test.cc
@@ -23,7 +23,9 @@
 
 // Inherit from Transform so we have access to protected methods
 struct CreateASTTypeForTest : public testing::Test, public Transform {
-    Output Run(const Program*, const DataMap&) const override { return {}; }
+    ApplyResult Apply(const Program*, const DataMap&, DataMap&) const override {
+        return SkipTransform;
+    }
 
     const ast::Type* create(std::function<sem::Type*(ProgramBuilder&)> create_sem_type) {
         ProgramBuilder sem_type_builder;
diff --git a/src/tint/transform/unshadow.cc b/src/tint/transform/unshadow.cc
index 975e2ed..93ce595 100644
--- a/src/tint/transform/unshadow.cc
+++ b/src/tint/transform/unshadow.cc
@@ -28,27 +28,32 @@
 
 namespace tint::transform {
 
-/// The PIMPL state for the Unshadow transform
+/// PIMPL state for the transform
 struct Unshadow::State {
+    /// The source program
+    const Program* const src;
+    /// The target program builder
+    ProgramBuilder b;
     /// The clone context
-    CloneContext& ctx;
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
 
     /// Constructor
-    /// @param context the clone context
-    explicit State(CloneContext& context) : ctx(context) {}
+    /// @param program the source program
+    explicit State(const Program* program) : src(program) {}
 
-    /// Performs the transformation
-    void Run() {
-        auto& sem = ctx.src->Sem();
+    /// Runs the transform
+    /// @returns the new program or SkipTransform if the transform is not required
+    Transform::ApplyResult Run() {
+        auto& sem = src->Sem();
 
         // Maps a variable to its new name.
-        std::unordered_map<const sem::Variable*, Symbol> renamed_to;
+        utils::Hashmap<const sem::Variable*, Symbol, 8> renamed_to;
 
         auto rename = [&](const sem::Variable* v) -> const ast::Variable* {
             auto* decl = v->Declaration();
-            auto name = ctx.src->Symbols().NameFor(decl->symbol);
-            auto symbol = ctx.dst->Symbols().New(name);
-            renamed_to.emplace(v, symbol);
+            auto name = src->Symbols().NameFor(decl->symbol);
+            auto symbol = b.Symbols().New(name);
+            renamed_to.Add(v, symbol);
 
             auto source = ctx.Clone(decl->source);
             auto* type = ctx.Clone(decl->type);
@@ -57,20 +62,20 @@
             return Switch(
                 decl,  //
                 [&](const ast::Var* var) {
-                    return ctx.dst->Var(source, symbol, type, var->declared_address_space,
-                                        var->declared_access, initializer, attributes);
+                    return b.Var(source, symbol, type, var->declared_address_space,
+                                 var->declared_access, initializer, attributes);
                 },
                 [&](const ast::Let*) {
-                    return ctx.dst->Let(source, symbol, type, initializer, attributes);
+                    return b.Let(source, symbol, type, initializer, attributes);
                 },
                 [&](const ast::Const*) {
-                    return ctx.dst->Const(source, symbol, type, initializer, attributes);
+                    return b.Const(source, symbol, type, initializer, attributes);
                 },
-                [&](const ast::Parameter*) {
-                    return ctx.dst->Param(source, symbol, type, attributes);
+                [&](const ast::Parameter*) {  //
+                    return b.Param(source, symbol, type, attributes);
                 },
                 [&](Default) {
-                    TINT_ICE(Transform, ctx.dst->Diagnostics())
+                    TINT_ICE(Transform, b.Diagnostics())
                         << "unexpected variable type: " << decl->TypeInfo().name;
                     return nullptr;
                 });
@@ -92,14 +97,15 @@
         ctx.ReplaceAll(
             [&](const ast::IdentifierExpression* ident) -> const tint::ast::IdentifierExpression* {
                 if (auto* user = sem.Get<sem::VariableUser>(ident)) {
-                    auto it = renamed_to.find(user->Variable());
-                    if (it != renamed_to.end()) {
-                        return ctx.dst->Expr(it->second);
+                    if (auto* renamed = renamed_to.Find(user->Variable())) {
+                        return b.Expr(*renamed);
                     }
                 }
                 return nullptr;
             });
+
         ctx.Clone();
+        return Program(std::move(b));
     }
 };
 
@@ -107,8 +113,8 @@
 
 Unshadow::~Unshadow() = default;
 
-void Unshadow::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    State(ctx).Run();
+Transform::ApplyResult Unshadow::Apply(const Program* src, const DataMap&, DataMap&) const {
+    return State(src).Run();
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/unshadow.h b/src/tint/transform/unshadow.h
index 5ffe839..8ebf105 100644
--- a/src/tint/transform/unshadow.h
+++ b/src/tint/transform/unshadow.h
@@ -29,16 +29,13 @@
     /// Destructor
     ~Unshadow() override;
 
-  protected:
-    struct State;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+  private:
+    struct State;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/unwind_discard_functions.cc b/src/tint/transform/unwind_discard_functions.cc
index 4e20d55..068fe35 100644
--- a/src/tint/transform/unwind_discard_functions.cc
+++ b/src/tint/transform/unwind_discard_functions.cc
@@ -35,7 +35,51 @@
 namespace tint::transform {
 namespace {
 
-class State {
+bool ShouldRun(const Program* program) {
+    auto& sem = program->Sem();
+    for (auto* f : program->AST().Functions()) {
+        if (sem.Get(f)->Behaviors().Contains(sem::Behavior::kDiscard)) {
+            return true;
+        }
+    }
+    return false;
+}
+
+}  // namespace
+
+/// PIMPL state for the transform
+struct UnwindDiscardFunctions::State {
+    /// Constructor
+    /// @param ctx_in the context
+    explicit State(CloneContext& ctx_in) : ctx(ctx_in), b(*ctx_in.dst), sem(ctx_in.src->Sem()) {}
+
+    /// Runs the transform
+    void Run() {
+        ctx.ReplaceAll([&](const ast::BlockStatement* block) -> const ast::Statement* {
+            // Iterate block statements and replace them as needed.
+            for (auto* stmt : block->statements) {
+                if (auto* new_stmt = Statement(stmt)) {
+                    ctx.Replace(stmt, new_stmt);
+                }
+
+                // Handle for loops, as they are the only other AST node that
+                // contains statements outside of BlockStatements.
+                if (auto* fl = stmt->As<ast::ForLoopStatement>()) {
+                    if (auto* new_stmt = Statement(fl->initializer)) {
+                        ctx.Replace(fl->initializer, new_stmt);
+                    }
+                    if (auto* new_stmt = Statement(fl->continuing)) {
+                        // NOTE: Should never reach here as we cannot discard in a
+                        // continuing block.
+                        ctx.Replace(fl->continuing, new_stmt);
+                    }
+                }
+            }
+
+            return nullptr;
+        });
+    }
+
   private:
     CloneContext& ctx;
     ProgramBuilder& b;
@@ -163,7 +207,7 @@
     // Returns true if `stmt` is a for-loop initializer statement.
     bool IsForLoopInitStatement(const ast::Statement* stmt) {
         if (auto* sem_stmt = sem.Get(stmt)) {
-            if (auto* sem_fl = As<sem::ForLoopStatement>(sem_stmt->Parent())) {
+            if (auto* sem_fl = tint::As<sem::ForLoopStatement>(sem_stmt->Parent())) {
                 return sem_fl->Declaration()->initializer == stmt;
             }
         }
@@ -305,60 +349,26 @@
                 return TryInsertAfter(s, sem_expr);
             });
     }
-
-  public:
-    /// Constructor
-    /// @param ctx_in the context
-    explicit State(CloneContext& ctx_in) : ctx(ctx_in), b(*ctx_in.dst), sem(ctx_in.src->Sem()) {}
-
-    /// Runs the transform
-    void Run() {
-        ctx.ReplaceAll([&](const ast::BlockStatement* block) -> const ast::Statement* {
-            // Iterate block statements and replace them as needed.
-            for (auto* stmt : block->statements) {
-                if (auto* new_stmt = Statement(stmt)) {
-                    ctx.Replace(stmt, new_stmt);
-                }
-
-                // Handle for loops, as they are the only other AST node that
-                // contains statements outside of BlockStatements.
-                if (auto* fl = stmt->As<ast::ForLoopStatement>()) {
-                    if (auto* new_stmt = Statement(fl->initializer)) {
-                        ctx.Replace(fl->initializer, new_stmt);
-                    }
-                    if (auto* new_stmt = Statement(fl->continuing)) {
-                        // NOTE: Should never reach here as we cannot discard in a
-                        // continuing block.
-                        ctx.Replace(fl->continuing, new_stmt);
-                    }
-                }
-            }
-
-            return nullptr;
-        });
-
-        ctx.Clone();
-    }
 };
 
-}  // namespace
-
 UnwindDiscardFunctions::UnwindDiscardFunctions() = default;
 UnwindDiscardFunctions::~UnwindDiscardFunctions() = default;
 
-void UnwindDiscardFunctions::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+Transform::ApplyResult UnwindDiscardFunctions::Apply(const Program* src,
+                                                     const DataMap&,
+                                                     DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
+    }
+
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     State state(ctx);
     state.Run();
-}
 
-bool UnwindDiscardFunctions::ShouldRun(const Program* program, const DataMap& /*data*/) const {
-    auto& sem = program->Sem();
-    for (auto* f : program->AST().Functions()) {
-        if (sem.Get(f)->Behaviors().Contains(sem::Behavior::kDiscard)) {
-            return true;
-        }
-    }
-    return false;
+    ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/unwind_discard_functions.h b/src/tint/transform/unwind_discard_functions.h
index 105a9d8..7614c27 100644
--- a/src/tint/transform/unwind_discard_functions.h
+++ b/src/tint/transform/unwind_discard_functions.h
@@ -44,19 +44,13 @@
     /// Destructor
     ~UnwindDiscardFunctions() override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
+  private:
+    struct State;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/utils/hoist_to_decl_before.cc b/src/tint/transform/utils/hoist_to_decl_before.cc
index 0aed996..e0b35a1 100644
--- a/src/tint/transform/utils/hoist_to_decl_before.cc
+++ b/src/tint/transform/utils/hoist_to_decl_before.cc
@@ -30,7 +30,59 @@
 namespace tint::transform {
 
 /// Private implementation of HoistToDeclBefore transform
-class HoistToDeclBefore::State {
+struct HoistToDeclBefore::State {
+    /// Constructor
+    /// @param ctx_in the clone context
+    explicit State(CloneContext& ctx_in) : ctx(ctx_in), b(*ctx_in.dst) {}
+
+    /// @copydoc HoistToDeclBefore::Add()
+    bool Add(const sem::Expression* before_expr,
+             const ast::Expression* expr,
+             bool as_let,
+             const char* decl_name) {
+        auto name = b.Symbols().New(decl_name);
+
+        if (as_let) {
+            auto builder = [this, expr, name] {
+                return b.Decl(b.Let(name, ctx.CloneWithoutTransform(expr)));
+            };
+            if (!InsertBeforeImpl(before_expr->Stmt(), std::move(builder))) {
+                return false;
+            }
+        } else {
+            auto builder = [this, expr, name] {
+                return b.Decl(b.Var(name, ctx.CloneWithoutTransform(expr)));
+            };
+            if (!InsertBeforeImpl(before_expr->Stmt(), std::move(builder))) {
+                return false;
+            }
+        }
+
+        // Replace the initializer expression with a reference to the let
+        ctx.Replace(expr, b.Expr(name));
+        return true;
+    }
+
+    /// @copydoc HoistToDeclBefore::InsertBefore(const sem::Statement*, const ast::Statement*)
+    bool InsertBefore(const sem::Statement* before_stmt, const ast::Statement* stmt) {
+        if (stmt) {
+            auto builder = [stmt] { return stmt; };
+            return InsertBeforeImpl(before_stmt, std::move(builder));
+        }
+        return InsertBeforeImpl(before_stmt, Decompose{});
+    }
+
+    /// @copydoc HoistToDeclBefore::InsertBefore(const sem::Statement*, const StmtBuilder&)
+    bool InsertBefore(const sem::Statement* before_stmt, const StmtBuilder& builder) {
+        return InsertBeforeImpl(before_stmt, std::move(builder));
+    }
+
+    /// @copydoc HoistToDeclBefore::Prepare()
+    bool Prepare(const sem::Expression* before_expr) {
+        return InsertBefore(before_expr->Stmt(), nullptr);
+    }
+
+  private:
     CloneContext& ctx;
     ProgramBuilder& b;
 
@@ -215,6 +267,8 @@
 
     template <typename BUILDER>
     bool InsertBeforeImpl(const sem::Statement* before_stmt, BUILDER&& builder) {
+        (void)builder;  // Avoid 'unused parameter' warning due to 'if constexpr'
+
         auto* ip = before_stmt->Declaration();
 
         auto* else_if = before_stmt->As<sem::IfStatement>();
@@ -299,58 +353,6 @@
             << "unhandled expression parent statement type: " << parent->TypeInfo().name;
         return false;
     }
-
-  public:
-    /// Constructor
-    /// @param ctx_in the clone context
-    explicit State(CloneContext& ctx_in) : ctx(ctx_in), b(*ctx_in.dst) {}
-
-    /// @copydoc HoistToDeclBefore::Add()
-    bool Add(const sem::Expression* before_expr,
-             const ast::Expression* expr,
-             bool as_let,
-             const char* decl_name) {
-        auto name = b.Symbols().New(decl_name);
-
-        if (as_let) {
-            auto builder = [this, expr, name] {
-                return b.Decl(b.Let(name, ctx.CloneWithoutTransform(expr)));
-            };
-            if (!InsertBeforeImpl(before_expr->Stmt(), std::move(builder))) {
-                return false;
-            }
-        } else {
-            auto builder = [this, expr, name] {
-                return b.Decl(b.Var(name, ctx.CloneWithoutTransform(expr)));
-            };
-            if (!InsertBeforeImpl(before_expr->Stmt(), std::move(builder))) {
-                return false;
-            }
-        }
-
-        // Replace the initializer expression with a reference to the let
-        ctx.Replace(expr, b.Expr(name));
-        return true;
-    }
-
-    /// @copydoc HoistToDeclBefore::InsertBefore(const sem::Statement*, const ast::Statement*)
-    bool InsertBefore(const sem::Statement* before_stmt, const ast::Statement* stmt) {
-        if (stmt) {
-            auto builder = [stmt] { return stmt; };
-            return InsertBeforeImpl(before_stmt, std::move(builder));
-        }
-        return InsertBeforeImpl(before_stmt, Decompose{});
-    }
-
-    /// @copydoc HoistToDeclBefore::InsertBefore(const sem::Statement*, const StmtBuilder&)
-    bool InsertBefore(const sem::Statement* before_stmt, const StmtBuilder& builder) {
-        return InsertBeforeImpl(before_stmt, std::move(builder));
-    }
-
-    /// @copydoc HoistToDeclBefore::Prepare()
-    bool Prepare(const sem::Expression* before_expr) {
-        return InsertBefore(before_expr->Stmt(), nullptr);
-    }
 };
 
 HoistToDeclBefore::HoistToDeclBefore(CloneContext& ctx) : state_(std::make_unique<State>(ctx)) {}
diff --git a/src/tint/transform/utils/hoist_to_decl_before.h b/src/tint/transform/utils/hoist_to_decl_before.h
index b2e993e..d9a8a8a 100644
--- a/src/tint/transform/utils/hoist_to_decl_before.h
+++ b/src/tint/transform/utils/hoist_to_decl_before.h
@@ -77,7 +77,7 @@
     bool Prepare(const sem::Expression* before_expr);
 
   private:
-    class State;
+    struct State;
     std::unique_ptr<State> state_;
 };
 
diff --git a/src/tint/transform/var_for_dynamic_index.cc b/src/tint/transform/var_for_dynamic_index.cc
index d30831e..81af013 100644
--- a/src/tint/transform/var_for_dynamic_index.cc
+++ b/src/tint/transform/var_for_dynamic_index.cc
@@ -13,6 +13,9 @@
 // limitations under the License.
 
 #include "src/tint/transform/var_for_dynamic_index.h"
+
+#include <utility>
+
 #include "src/tint/program_builder.h"
 #include "src/tint/transform/utils/hoist_to_decl_before.h"
 
@@ -22,7 +25,12 @@
 
 VarForDynamicIndex::~VarForDynamicIndex() = default;
 
-void VarForDynamicIndex::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+Transform::ApplyResult VarForDynamicIndex::Apply(const Program* src,
+                                                 const DataMap&,
+                                                 DataMap&) const {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     HoistToDeclBefore hoist_to_decl_before(ctx);
 
     // Extracts array and matrix values that are dynamically indexed to a
@@ -30,7 +38,7 @@
     auto dynamic_index_to_var = [&](const ast::IndexAccessorExpression* access_expr) {
         auto* index_expr = access_expr->index;
         auto* object_expr = access_expr->object;
-        auto& sem = ctx.src->Sem();
+        auto& sem = src->Sem();
 
         if (sem.Get(index_expr)->ConstantValue()) {
             // Index expression resolves to a compile time value.
@@ -49,15 +57,21 @@
         return hoist_to_decl_before.Add(indexed, object_expr, false, "var_for_index");
     };
 
-    for (auto* node : ctx.src->ASTNodes().Objects()) {
+    bool index_accessor_found = false;
+    for (auto* node : src->ASTNodes().Objects()) {
         if (auto* access_expr = node->As<ast::IndexAccessorExpression>()) {
             if (!dynamic_index_to_var(access_expr)) {
-                return;
+                return Program(std::move(b));
             }
+            index_accessor_found = true;
         }
     }
+    if (!index_accessor_found) {
+        return SkipTransform;
+    }
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/var_for_dynamic_index.h b/src/tint/transform/var_for_dynamic_index.h
index 39ef2f2..070a2cd 100644
--- a/src/tint/transform/var_for_dynamic_index.h
+++ b/src/tint/transform/var_for_dynamic_index.h
@@ -31,14 +31,10 @@
     /// Destructor
     ~VarForDynamicIndex() override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/vectorize_matrix_conversions.cc b/src/tint/transform/vectorize_matrix_conversions.cc
index 576b885..94fbdf3 100644
--- a/src/tint/transform/vectorize_matrix_conversions.cc
+++ b/src/tint/transform/vectorize_matrix_conversions.cc
@@ -30,11 +30,9 @@
 
 namespace tint::transform {
 
-VectorizeMatrixConversions::VectorizeMatrixConversions() = default;
+namespace {
 
-VectorizeMatrixConversions::~VectorizeMatrixConversions() = default;
-
-bool VectorizeMatrixConversions::ShouldRun(const Program* program, const DataMap&) const {
+bool ShouldRun(const Program* program) {
     for (auto* node : program->ASTNodes().Objects()) {
         if (auto* sem = program->Sem().Get<sem::Expression>(node)) {
             if (auto* call = sem->UnwrapMaterialize()->As<sem::Call>()) {
@@ -50,14 +48,29 @@
     return false;
 }
 
-void VectorizeMatrixConversions::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+}  // namespace
+
+VectorizeMatrixConversions::VectorizeMatrixConversions() = default;
+
+VectorizeMatrixConversions::~VectorizeMatrixConversions() = default;
+
+Transform::ApplyResult VectorizeMatrixConversions::Apply(const Program* src,
+                                                         const DataMap&,
+                                                         DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
+    }
+
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     using HelperFunctionKey =
         utils::UnorderedKeyWrapper<std::tuple<const sem::Matrix*, const sem::Matrix*>>;
 
     std::unordered_map<HelperFunctionKey, Symbol> matrix_convs;
 
     ctx.ReplaceAll([&](const ast::CallExpression* expr) -> const ast::CallExpression* {
-        auto* call = ctx.src->Sem().Get(expr)->UnwrapMaterialize()->As<sem::Call>();
+        auto* call = src->Sem().Get(expr)->UnwrapMaterialize()->As<sem::Call>();
         auto* ty_conv = call->Target()->As<sem::TypeConversion>();
         if (!ty_conv) {
             return nullptr;
@@ -72,16 +85,16 @@
             return nullptr;
         }
 
-        auto& src = args[0];
+        auto& matrix = args[0];
 
-        auto* src_type = args[0]->Type()->UnwrapRef()->As<sem::Matrix>();
+        auto* src_type = matrix->Type()->UnwrapRef()->As<sem::Matrix>();
         if (!src_type) {
             return nullptr;
         }
 
         // The source and destination type of a matrix conversion must have a same shape.
         if (!(src_type->rows() == dst_type->rows() && src_type->columns() == dst_type->columns())) {
-            TINT_ICE(Transform, ctx.dst->Diagnostics())
+            TINT_ICE(Transform, b.Diagnostics())
                 << "source and destination matrix has different shape in matrix conversion";
             return nullptr;
         }
@@ -90,47 +103,45 @@
             utils::Vector<const ast::Expression*, 4> columns;
             for (uint32_t c = 0; c < dst_type->columns(); c++) {
                 auto* src_matrix_expr = src_expression_builder();
-                auto* src_column_expr =
-                    ctx.dst->IndexAccessor(src_matrix_expr, ctx.dst->Expr(tint::AInt(c)));
-                columns.Push(ctx.dst->Construct(CreateASTTypeFor(ctx, dst_type->ColumnType()),
-                                                src_column_expr));
+                auto* src_column_expr = b.IndexAccessor(src_matrix_expr, b.Expr(tint::AInt(c)));
+                columns.Push(
+                    b.Construct(CreateASTTypeFor(ctx, dst_type->ColumnType()), src_column_expr));
             }
-            return ctx.dst->Construct(CreateASTTypeFor(ctx, dst_type), columns);
+            return b.Construct(CreateASTTypeFor(ctx, dst_type), columns);
         };
 
         // Replace the matrix conversion to column vector conversions and a matrix construction.
-        if (!src->HasSideEffects()) {
+        if (!matrix->HasSideEffects()) {
             // Simply use the argument's declaration if it has no side effects.
             return build_vectorized_conversion_expression([&]() {  //
-                return ctx.Clone(src->Declaration());
+                return ctx.Clone(matrix->Declaration());
             });
         } else {
             // If has side effects, use a helper function.
             auto fn =
                 utils::GetOrCreate(matrix_convs, HelperFunctionKey{{src_type, dst_type}}, [&] {
-                    auto name =
-                        ctx.dst->Symbols().New("convert_mat" + std::to_string(src_type->columns()) +
-                                               "x" + std::to_string(src_type->rows()) + "_" +
-                                               ctx.dst->FriendlyName(src_type->type()) + "_" +
-                                               ctx.dst->FriendlyName(dst_type->type()));
-                    ctx.dst->Func(
-                        name,
-                        utils::Vector{
-                            ctx.dst->Param("value", CreateASTTypeFor(ctx, src_type)),
-                        },
-                        CreateASTTypeFor(ctx, dst_type),
-                        utils::Vector{
-                            ctx.dst->Return(build_vectorized_conversion_expression([&]() {  //
-                                return ctx.dst->Expr("value");
-                            })),
-                        });
+                    auto name = b.Symbols().New(
+                        "convert_mat" + std::to_string(src_type->columns()) + "x" +
+                        std::to_string(src_type->rows()) + "_" + b.FriendlyName(src_type->type()) +
+                        "_" + b.FriendlyName(dst_type->type()));
+                    b.Func(name,
+                           utils::Vector{
+                               b.Param("value", CreateASTTypeFor(ctx, src_type)),
+                           },
+                           CreateASTTypeFor(ctx, dst_type),
+                           utils::Vector{
+                               b.Return(build_vectorized_conversion_expression([&]() {  //
+                                   return b.Expr("value");
+                               })),
+                           });
                     return name;
                 });
-            return ctx.dst->Call(fn, ctx.Clone(args[0]->Declaration()));
+            return b.Call(fn, ctx.Clone(args[0]->Declaration()));
         }
     });
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/vectorize_matrix_conversions.h b/src/tint/transform/vectorize_matrix_conversions.h
index f16467c..c86240c 100644
--- a/src/tint/transform/vectorize_matrix_conversions.h
+++ b/src/tint/transform/vectorize_matrix_conversions.h
@@ -28,19 +28,10 @@
     /// Destructor
     ~VectorizeMatrixConversions() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/vectorize_scalar_matrix_initializers.cc b/src/tint/transform/vectorize_scalar_matrix_initializers.cc
index 97b0e4f..e6e1c46 100644
--- a/src/tint/transform/vectorize_scalar_matrix_initializers.cc
+++ b/src/tint/transform/vectorize_scalar_matrix_initializers.cc
@@ -27,12 +27,9 @@
 TINT_INSTANTIATE_TYPEINFO(tint::transform::VectorizeScalarMatrixInitializers);
 
 namespace tint::transform {
+namespace {
 
-VectorizeScalarMatrixInitializers::VectorizeScalarMatrixInitializers() = default;
-
-VectorizeScalarMatrixInitializers::~VectorizeScalarMatrixInitializers() = default;
-
-bool VectorizeScalarMatrixInitializers::ShouldRun(const Program* program, const DataMap&) const {
+bool ShouldRun(const Program* program) {
     for (auto* node : program->ASTNodes().Objects()) {
         if (auto* call = program->Sem().Get<sem::Call>(node)) {
             if (call->Target()->Is<sem::TypeInitializer>() && call->Type()->Is<sem::Matrix>()) {
@@ -46,11 +43,26 @@
     return false;
 }
 
-void VectorizeScalarMatrixInitializers::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+}  // namespace
+
+VectorizeScalarMatrixInitializers::VectorizeScalarMatrixInitializers() = default;
+
+VectorizeScalarMatrixInitializers::~VectorizeScalarMatrixInitializers() = default;
+
+Transform::ApplyResult VectorizeScalarMatrixInitializers::Apply(const Program* src,
+                                                                const DataMap&,
+                                                                DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
+    }
+
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     std::unordered_map<const sem::Matrix*, Symbol> scalar_inits;
 
     ctx.ReplaceAll([&](const ast::CallExpression* expr) -> const ast::CallExpression* {
-        auto* call = ctx.src->Sem().Get(expr)->UnwrapMaterialize()->As<sem::Call>();
+        auto* call = src->Sem().Get(expr)->UnwrapMaterialize()->As<sem::Call>();
         auto* ty_init = call->Target()->As<sem::TypeInitializer>();
         if (!ty_init) {
             return nullptr;
@@ -87,10 +99,10 @@
                 }
 
                 // Construct the column vector.
-                columns.Push(ctx.dst->vec(CreateASTTypeFor(ctx, mat_type->type()), mat_type->rows(),
-                                          std::move(row_values)));
+                columns.Push(b.vec(CreateASTTypeFor(ctx, mat_type->type()), mat_type->rows(),
+                                   std::move(row_values)));
             }
-            return ctx.dst->Construct(CreateASTTypeFor(ctx, mat_type), columns);
+            return b.Construct(CreateASTTypeFor(ctx, mat_type), columns);
         };
 
         if (args.Length() == 1) {
@@ -98,23 +110,22 @@
             // This is done to ensure that the single argument value is only evaluated once, and
             // with the correct expression evaluation order.
             auto fn = utils::GetOrCreate(scalar_inits, mat_type, [&] {
-                auto name =
-                    ctx.dst->Symbols().New("build_mat" + std::to_string(mat_type->columns()) + "x" +
-                                           std::to_string(mat_type->rows()));
-                ctx.dst->Func(name,
-                              utils::Vector{
-                                  // Single scalar parameter
-                                  ctx.dst->Param("value", CreateASTTypeFor(ctx, mat_type->type())),
-                              },
-                              CreateASTTypeFor(ctx, mat_type),
-                              utils::Vector{
-                                  ctx.dst->Return(build_mat([&](uint32_t, uint32_t) {  //
-                                      return ctx.dst->Expr("value");
-                                  })),
-                              });
+                auto name = b.Symbols().New("build_mat" + std::to_string(mat_type->columns()) +
+                                            "x" + std::to_string(mat_type->rows()));
+                b.Func(name,
+                       utils::Vector{
+                           // Single scalar parameter
+                           b.Param("value", CreateASTTypeFor(ctx, mat_type->type())),
+                       },
+                       CreateASTTypeFor(ctx, mat_type),
+                       utils::Vector{
+                           b.Return(build_mat([&](uint32_t, uint32_t) {  //
+                               return b.Expr("value");
+                           })),
+                       });
                 return name;
             });
-            return ctx.dst->Call(fn, ctx.Clone(args[0]->Declaration()));
+            return b.Call(fn, ctx.Clone(args[0]->Declaration()));
         }
 
         if (args.Length() == mat_type->columns() * mat_type->rows()) {
@@ -123,12 +134,13 @@
             });
         }
 
-        TINT_ICE(Transform, ctx.dst->Diagnostics())
+        TINT_ICE(Transform, b.Diagnostics())
             << "matrix initializer has unexpected number of arguments";
         return nullptr;
     });
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/vectorize_scalar_matrix_initializers.h b/src/tint/transform/vectorize_scalar_matrix_initializers.h
index 342754a..f9c0164 100644
--- a/src/tint/transform/vectorize_scalar_matrix_initializers.h
+++ b/src/tint/transform/vectorize_scalar_matrix_initializers.h
@@ -29,19 +29,10 @@
     /// Destructor
     ~VectorizeScalarMatrixInitializers() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/vertex_pulling.cc b/src/tint/transform/vertex_pulling.cc
index 00b5a06..d5ee424 100644
--- a/src/tint/transform/vertex_pulling.cc
+++ b/src/tint/transform/vertex_pulling.cc
@@ -201,13 +201,46 @@
     return {BaseType::kInvalid, 0};
 }
 
-struct State {
-    State(CloneContext& context, const VertexPulling::Config& c) : ctx(context), cfg(c) {}
-    State(const State&) = default;
-    ~State() = default;
+}  // namespace
 
-    /// LocationReplacement describes an ast::Variable replacement for a
-    /// location input.
+/// PIMPL state for the transform
+struct VertexPulling::State {
+    /// Constructor
+    /// @param program the source program
+    /// @param c the VertexPulling config
+    State(const Program* program, const VertexPulling::Config& c) : src(program), cfg(c) {}
+
+    /// Runs the transform
+    /// @returns the new program or SkipTransform if the transform is not required
+    ApplyResult Run() {
+        // Find entry point
+        const ast::Function* func = nullptr;
+        for (auto* fn : src->AST().Functions()) {
+            if (fn->PipelineStage() == ast::PipelineStage::kVertex) {
+                if (func != nullptr) {
+                    b.Diagnostics().add_error(
+                        diag::System::Transform,
+                        "VertexPulling found more than one vertex entry point");
+                    return Program(std::move(b));
+                }
+                func = fn;
+            }
+        }
+        if (func == nullptr) {
+            b.Diagnostics().add_error(diag::System::Transform,
+                                      "Vertex stage entry point not found");
+            return Program(std::move(b));
+        }
+
+        AddVertexStorageBuffers();
+        Process(func);
+
+        ctx.Clone();
+        return Program(std::move(b));
+    }
+
+  private:
+    /// LocationReplacement describes an ast::Variable replacement for a location input.
     struct LocationReplacement {
         /// The variable to replace in the source Program
         ast::Variable* from;
@@ -215,13 +248,22 @@
         ast::Variable* to;
     };
 
+    /// LocationInfo describes an input location
     struct LocationInfo {
+        /// A builder that builds the expression that resolves to the (transformed) input location
         std::function<const ast::Expression*()> expr;
+        /// The store type of the location variable
         const sem::Type* type;
     };
 
-    CloneContext& ctx;
+    /// The source program
+    const Program* const src;
+    /// The transform config
     VertexPulling::Config const cfg;
+    /// The target program builder
+    ProgramBuilder b;
+    /// The clone context
+    CloneContext ctx = {&b, src, /* auto_clone_symbols */ true};
     std::unordered_map<uint32_t, LocationInfo> location_info;
     std::function<const ast::Expression*()> vertex_index_expr = nullptr;
     std::function<const ast::Expression*()> instance_index_expr = nullptr;
@@ -235,7 +277,7 @@
     Symbol GetVertexBufferName(uint32_t index) {
         return utils::GetOrCreate(vertex_buffer_names, index, [&] {
             static const char kVertexBufferNamePrefix[] = "tint_pulling_vertex_buffer_";
-            return ctx.dst->Symbols().New(kVertexBufferNamePrefix + std::to_string(index));
+            return b.Symbols().New(kVertexBufferNamePrefix + std::to_string(index));
         });
     }
 
@@ -243,7 +285,7 @@
     Symbol GetStructBufferName() {
         if (!struct_buffer_name.IsValid()) {
             static const char kStructBufferName[] = "tint_vertex_data";
-            struct_buffer_name = ctx.dst->Symbols().New(kStructBufferName);
+            struct_buffer_name = b.Symbols().New(kStructBufferName);
         }
         return struct_buffer_name;
     }
@@ -252,21 +294,19 @@
     void AddVertexStorageBuffers() {
         // Creating the struct type
         static const char kStructName[] = "TintVertexData";
-        auto* struct_type =
-            ctx.dst->Structure(ctx.dst->Symbols().New(kStructName),
-                               utils::Vector{
-                                   ctx.dst->Member(GetStructBufferName(), ctx.dst->ty.array<u32>()),
-                               });
+        auto* struct_type = b.Structure(b.Symbols().New(kStructName),
+                                        utils::Vector{
+                                            b.Member(GetStructBufferName(), b.ty.array<u32>()),
+                                        });
         for (uint32_t i = 0; i < cfg.vertex_state.size(); ++i) {
             // The decorated variable with struct type
-            ctx.dst->GlobalVar(GetVertexBufferName(i), ctx.dst->ty.Of(struct_type),
-                               ast::AddressSpace::kStorage, ast::Access::kRead,
-                               ctx.dst->Binding(AInt(i)), ctx.dst->Group(AInt(cfg.pulling_group)));
+            b.GlobalVar(GetVertexBufferName(i), b.ty.Of(struct_type), ast::AddressSpace::kStorage,
+                        ast::Access::kRead, b.Binding(AInt(i)), b.Group(AInt(cfg.pulling_group)));
         }
     }
 
     /// Creates and returns the assignment to the variables from the buffers
-    ast::BlockStatement* CreateVertexPullingPreamble() {
+    const ast::BlockStatement* CreateVertexPullingPreamble() {
         // Assign by looking at the vertex descriptor to find attributes with
         // matching location.
 
@@ -276,7 +316,7 @@
             const VertexBufferLayoutDescriptor& buffer_layout = cfg.vertex_state[buffer_idx];
 
             if ((buffer_layout.array_stride & 3) != 0) {
-                ctx.dst->Diagnostics().add_error(
+                b.Diagnostics().add_error(
                     diag::System::Transform,
                     "WebGPU requires that vertex stride must be a multiple of 4 bytes, "
                     "but VertexPulling array stride for buffer " +
@@ -292,15 +332,15 @@
             // buffer_array_base is the base array offset for all the vertex
             // attributes. These are units of uint (4 bytes).
             auto buffer_array_base =
-                ctx.dst->Symbols().New("buffer_array_base_" + std::to_string(buffer_idx));
+                b.Symbols().New("buffer_array_base_" + std::to_string(buffer_idx));
 
             auto* attribute_offset = index_expr;
             if (buffer_layout.array_stride != 4) {
-                attribute_offset = ctx.dst->Mul(index_expr, u32(buffer_layout.array_stride / 4u));
+                attribute_offset = b.Mul(index_expr, u32(buffer_layout.array_stride / 4u));
             }
 
             // let pulling_offset_n = <attribute_offset>
-            stmts.Push(ctx.dst->Decl(ctx.dst->Let(buffer_array_base, attribute_offset)));
+            stmts.Push(b.Decl(b.Let(buffer_array_base, attribute_offset)));
 
             for (const VertexAttributeDescriptor& attribute_desc : buffer_layout.attributes) {
                 auto it = location_info.find(attribute_desc.shader_location);
@@ -320,8 +360,8 @@
                     err << "VertexAttributeDescriptor for location "
                         << std::to_string(attribute_desc.shader_location) << " has format "
                         << attribute_desc.format << " but shader expects "
-                        << var.type->FriendlyName(ctx.src->Symbols());
-                    ctx.dst->Diagnostics().add_error(diag::System::Transform, err.str());
+                        << var.type->FriendlyName(src->Symbols());
+                    b.Diagnostics().add_error(diag::System::Transform, err.str());
                     return nullptr;
                 }
 
@@ -337,16 +377,16 @@
                     // WGSL variable vector width is smaller than the loaded vector width
                     switch (var_dt.width) {
                         case 1:
-                            value = ctx.dst->MemberAccessor(fetch, "x");
+                            value = b.MemberAccessor(fetch, "x");
                             break;
                         case 2:
-                            value = ctx.dst->MemberAccessor(fetch, "xy");
+                            value = b.MemberAccessor(fetch, "xy");
                             break;
                         case 3:
-                            value = ctx.dst->MemberAccessor(fetch, "xyz");
+                            value = b.MemberAccessor(fetch, "xyz");
                             break;
                         default:
-                            TINT_UNREACHABLE(Transform, ctx.dst->Diagnostics()) << var_dt.width;
+                            TINT_UNREACHABLE(Transform, b.Diagnostics()) << var_dt.width;
                             return nullptr;
                     }
                 } else if (var_dt.width > fmt_dt.width) {
@@ -355,32 +395,32 @@
                     utils::Vector<const ast::Expression*, 8> values{fetch};
                     switch (var_dt.base_type) {
                         case BaseType::kI32:
-                            ty = ctx.dst->ty.i32();
+                            ty = b.ty.i32();
                             for (uint32_t i = fmt_dt.width; i < var_dt.width; i++) {
-                                values.Push(ctx.dst->Expr((i == 3) ? 1_i : 0_i));
+                                values.Push(b.Expr((i == 3) ? 1_i : 0_i));
                             }
                             break;
                         case BaseType::kU32:
-                            ty = ctx.dst->ty.u32();
+                            ty = b.ty.u32();
                             for (uint32_t i = fmt_dt.width; i < var_dt.width; i++) {
-                                values.Push(ctx.dst->Expr((i == 3) ? 1_u : 0_u));
+                                values.Push(b.Expr((i == 3) ? 1_u : 0_u));
                             }
                             break;
                         case BaseType::kF32:
-                            ty = ctx.dst->ty.f32();
+                            ty = b.ty.f32();
                             for (uint32_t i = fmt_dt.width; i < var_dt.width; i++) {
-                                values.Push(ctx.dst->Expr((i == 3) ? 1_f : 0_f));
+                                values.Push(b.Expr((i == 3) ? 1_f : 0_f));
                             }
                             break;
                         default:
-                            TINT_UNREACHABLE(Transform, ctx.dst->Diagnostics()) << var_dt.base_type;
+                            TINT_UNREACHABLE(Transform, b.Diagnostics()) << var_dt.base_type;
                             return nullptr;
                     }
-                    value = ctx.dst->Construct(ctx.dst->ty.vec(ty, var_dt.width), values);
+                    value = b.Construct(b.ty.vec(ty, var_dt.width), values);
                 }
 
                 // Assign the value to the WGSL variable
-                stmts.Push(ctx.dst->Assign(var.expr(), value));
+                stmts.Push(b.Assign(var.expr(), value));
             }
         }
 
@@ -388,7 +428,7 @@
             return nullptr;
         }
 
-        return ctx.dst->create<ast::BlockStatement>(std::move(stmts));
+        return b.Block(std::move(stmts));
     }
 
     /// Generates an expression reading from a buffer a specific format.
@@ -407,7 +447,7 @@
         };
 
         // Returns a i32 loaded from buffer_base + offset.
-        auto load_i32 = [&] { return ctx.dst->Bitcast<i32>(load_u32()); };
+        auto load_i32 = [&] { return b.Bitcast<i32>(load_u32()); };
 
         // Returns a u32 loaded from buffer_base + offset + 4.
         auto load_next_u32 = [&] {
@@ -415,7 +455,7 @@
         };
 
         // Returns a i32 loaded from buffer_base + offset + 4.
-        auto load_next_i32 = [&] { return ctx.dst->Bitcast<i32>(load_next_u32()); };
+        auto load_next_i32 = [&] { return b.Bitcast<i32>(load_next_u32()); };
 
         // Returns a u16 loaded from offset, packed in the high 16 bits of a u32.
         // The low 16 bits are 0.
@@ -427,17 +467,17 @@
                 LoadPrimitive(array_base, low_u32_offset, buffer, VertexFormat::kUint32);
             switch (offset & 3) {
                 case 0:
-                    return ctx.dst->Shl(low_u32, 16_u);
+                    return b.Shl(low_u32, 16_u);
                 case 1:
-                    return ctx.dst->And(ctx.dst->Shl(low_u32, 8_u), 0xffff0000_u);
+                    return b.And(b.Shl(low_u32, 8_u), 0xffff0000_u);
                 case 2:
-                    return ctx.dst->And(low_u32, 0xffff0000_u);
+                    return b.And(low_u32, 0xffff0000_u);
                 default: {  // 3:
                     auto* high_u32 = LoadPrimitive(array_base, low_u32_offset + 4, buffer,
                                                    VertexFormat::kUint32);
-                    auto* shr = ctx.dst->Shr(low_u32, 8_u);
-                    auto* shl = ctx.dst->Shl(high_u32, 24_u);
-                    return ctx.dst->And(ctx.dst->Or(shl, shr), 0xffff0000_u);
+                    auto* shr = b.Shr(low_u32, 8_u);
+                    auto* shl = b.Shl(high_u32, 24_u);
+                    return b.And(b.Or(shl, shr), 0xffff0000_u);
                 }
             }
         };
@@ -450,24 +490,24 @@
                 LoadPrimitive(array_base, low_u32_offset, buffer, VertexFormat::kUint32);
             switch (offset & 3) {
                 case 0:
-                    return ctx.dst->And(low_u32, 0xffff_u);
+                    return b.And(low_u32, 0xffff_u);
                 case 1:
-                    return ctx.dst->And(ctx.dst->Shr(low_u32, 8_u), 0xffff_u);
+                    return b.And(b.Shr(low_u32, 8_u), 0xffff_u);
                 case 2:
-                    return ctx.dst->Shr(low_u32, 16_u);
+                    return b.Shr(low_u32, 16_u);
                 default: {  // 3:
                     auto* high_u32 = LoadPrimitive(array_base, low_u32_offset + 4, buffer,
                                                    VertexFormat::kUint32);
-                    auto* shr = ctx.dst->Shr(low_u32, 24_u);
-                    auto* shl = ctx.dst->Shl(high_u32, 8_u);
-                    return ctx.dst->And(ctx.dst->Or(shl, shr), 0xffff_u);
+                    auto* shr = b.Shr(low_u32, 24_u);
+                    auto* shl = b.Shl(high_u32, 8_u);
+                    return b.And(b.Or(shl, shr), 0xffff_u);
                 }
             }
         };
 
         // Returns a i16 loaded from offset, packed in the high 16 bits of a u32.
         // The low 16 bits are 0.
-        auto load_i16_h = [&] { return ctx.dst->Bitcast<i32>(load_u16_h()); };
+        auto load_i16_h = [&] { return b.Bitcast<i32>(load_u16_h()); };
 
         // Assumptions are made that alignment must be at least as large as the size
         // of a single component.
@@ -480,128 +520,121 @@
 
                 // Vectors of basic primitives
             case VertexFormat::kUint32x2:
-                return LoadVec(array_base, offset, buffer, 4, ctx.dst->ty.u32(),
-                               VertexFormat::kUint32, 2);
+                return LoadVec(array_base, offset, buffer, 4, b.ty.u32(), VertexFormat::kUint32, 2);
             case VertexFormat::kUint32x3:
-                return LoadVec(array_base, offset, buffer, 4, ctx.dst->ty.u32(),
-                               VertexFormat::kUint32, 3);
+                return LoadVec(array_base, offset, buffer, 4, b.ty.u32(), VertexFormat::kUint32, 3);
             case VertexFormat::kUint32x4:
-                return LoadVec(array_base, offset, buffer, 4, ctx.dst->ty.u32(),
-                               VertexFormat::kUint32, 4);
+                return LoadVec(array_base, offset, buffer, 4, b.ty.u32(), VertexFormat::kUint32, 4);
             case VertexFormat::kSint32x2:
-                return LoadVec(array_base, offset, buffer, 4, ctx.dst->ty.i32(),
-                               VertexFormat::kSint32, 2);
+                return LoadVec(array_base, offset, buffer, 4, b.ty.i32(), VertexFormat::kSint32, 2);
             case VertexFormat::kSint32x3:
-                return LoadVec(array_base, offset, buffer, 4, ctx.dst->ty.i32(),
-                               VertexFormat::kSint32, 3);
+                return LoadVec(array_base, offset, buffer, 4, b.ty.i32(), VertexFormat::kSint32, 3);
             case VertexFormat::kSint32x4:
-                return LoadVec(array_base, offset, buffer, 4, ctx.dst->ty.i32(),
-                               VertexFormat::kSint32, 4);
+                return LoadVec(array_base, offset, buffer, 4, b.ty.i32(), VertexFormat::kSint32, 4);
             case VertexFormat::kFloat32x2:
-                return LoadVec(array_base, offset, buffer, 4, ctx.dst->ty.f32(),
-                               VertexFormat::kFloat32, 2);
+                return LoadVec(array_base, offset, buffer, 4, b.ty.f32(), VertexFormat::kFloat32,
+                               2);
             case VertexFormat::kFloat32x3:
-                return LoadVec(array_base, offset, buffer, 4, ctx.dst->ty.f32(),
-                               VertexFormat::kFloat32, 3);
+                return LoadVec(array_base, offset, buffer, 4, b.ty.f32(), VertexFormat::kFloat32,
+                               3);
             case VertexFormat::kFloat32x4:
-                return LoadVec(array_base, offset, buffer, 4, ctx.dst->ty.f32(),
-                               VertexFormat::kFloat32, 4);
+                return LoadVec(array_base, offset, buffer, 4, b.ty.f32(), VertexFormat::kFloat32,
+                               4);
 
             case VertexFormat::kUint8x2: {
                 // yyxx0000, yyxx0000
-                auto* u16s = ctx.dst->vec2<u32>(load_u16_h());
+                auto* u16s = b.vec2<u32>(load_u16_h());
                 // xx000000, yyxx0000
-                auto* shl = ctx.dst->Shl(u16s, ctx.dst->vec2<u32>(8_u, 0_u));
+                auto* shl = b.Shl(u16s, b.vec2<u32>(8_u, 0_u));
                 // 000000xx, 000000yy
-                return ctx.dst->Shr(shl, ctx.dst->vec2<u32>(24_u));
+                return b.Shr(shl, b.vec2<u32>(24_u));
             }
             case VertexFormat::kUint8x4: {
                 // wwzzyyxx, wwzzyyxx, wwzzyyxx, wwzzyyxx
-                auto* u32s = ctx.dst->vec4<u32>(load_u32());
+                auto* u32s = b.vec4<u32>(load_u32());
                 // xx000000, yyxx0000, zzyyxx00, wwzzyyxx
-                auto* shl = ctx.dst->Shl(u32s, ctx.dst->vec4<u32>(24_u, 16_u, 8_u, 0_u));
+                auto* shl = b.Shl(u32s, b.vec4<u32>(24_u, 16_u, 8_u, 0_u));
                 // 000000xx, 000000yy, 000000zz, 000000ww
-                return ctx.dst->Shr(shl, ctx.dst->vec4<u32>(24_u));
+                return b.Shr(shl, b.vec4<u32>(24_u));
             }
             case VertexFormat::kUint16x2: {
                 // yyyyxxxx, yyyyxxxx
-                auto* u32s = ctx.dst->vec2<u32>(load_u32());
+                auto* u32s = b.vec2<u32>(load_u32());
                 // xxxx0000, yyyyxxxx
-                auto* shl = ctx.dst->Shl(u32s, ctx.dst->vec2<u32>(16_u, 0_u));
+                auto* shl = b.Shl(u32s, b.vec2<u32>(16_u, 0_u));
                 // 0000xxxx, 0000yyyy
-                return ctx.dst->Shr(shl, ctx.dst->vec2<u32>(16_u));
+                return b.Shr(shl, b.vec2<u32>(16_u));
             }
             case VertexFormat::kUint16x4: {
                 // yyyyxxxx, wwwwzzzz
-                auto* u32s = ctx.dst->vec2<u32>(load_u32(), load_next_u32());
+                auto* u32s = b.vec2<u32>(load_u32(), load_next_u32());
                 // yyyyxxxx, yyyyxxxx, wwwwzzzz, wwwwzzzz
-                auto* xxyy = ctx.dst->MemberAccessor(u32s, "xxyy");
+                auto* xxyy = b.MemberAccessor(u32s, "xxyy");
                 // xxxx0000, yyyyxxxx, zzzz0000, wwwwzzzz
-                auto* shl = ctx.dst->Shl(xxyy, ctx.dst->vec4<u32>(16_u, 0_u, 16_u, 0_u));
+                auto* shl = b.Shl(xxyy, b.vec4<u32>(16_u, 0_u, 16_u, 0_u));
                 // 0000xxxx, 0000yyyy, 0000zzzz, 0000wwww
-                return ctx.dst->Shr(shl, ctx.dst->vec4<u32>(16_u));
+                return b.Shr(shl, b.vec4<u32>(16_u));
             }
             case VertexFormat::kSint8x2: {
                 // yyxx0000, yyxx0000
-                auto* i16s = ctx.dst->vec2<i32>(load_i16_h());
+                auto* i16s = b.vec2<i32>(load_i16_h());
                 // xx000000, yyxx0000
-                auto* shl = ctx.dst->Shl(i16s, ctx.dst->vec2<u32>(8_u, 0_u));
+                auto* shl = b.Shl(i16s, b.vec2<u32>(8_u, 0_u));
                 // ssssssxx, ssssssyy
-                return ctx.dst->Shr(shl, ctx.dst->vec2<u32>(24_u));
+                return b.Shr(shl, b.vec2<u32>(24_u));
             }
             case VertexFormat::kSint8x4: {
                 // wwzzyyxx, wwzzyyxx, wwzzyyxx, wwzzyyxx
-                auto* i32s = ctx.dst->vec4<i32>(load_i32());
+                auto* i32s = b.vec4<i32>(load_i32());
                 // xx000000, yyxx0000, zzyyxx00, wwzzyyxx
-                auto* shl = ctx.dst->Shl(i32s, ctx.dst->vec4<u32>(24_u, 16_u, 8_u, 0_u));
+                auto* shl = b.Shl(i32s, b.vec4<u32>(24_u, 16_u, 8_u, 0_u));
                 // ssssssxx, ssssssyy, sssssszz, ssssssww
-                return ctx.dst->Shr(shl, ctx.dst->vec4<u32>(24_u));
+                return b.Shr(shl, b.vec4<u32>(24_u));
             }
             case VertexFormat::kSint16x2: {
                 // yyyyxxxx, yyyyxxxx
-                auto* i32s = ctx.dst->vec2<i32>(load_i32());
+                auto* i32s = b.vec2<i32>(load_i32());
                 // xxxx0000, yyyyxxxx
-                auto* shl = ctx.dst->Shl(i32s, ctx.dst->vec2<u32>(16_u, 0_u));
+                auto* shl = b.Shl(i32s, b.vec2<u32>(16_u, 0_u));
                 // ssssxxxx, ssssyyyy
-                return ctx.dst->Shr(shl, ctx.dst->vec2<u32>(16_u));
+                return b.Shr(shl, b.vec2<u32>(16_u));
             }
             case VertexFormat::kSint16x4: {
                 // yyyyxxxx, wwwwzzzz
-                auto* i32s = ctx.dst->vec2<i32>(load_i32(), load_next_i32());
+                auto* i32s = b.vec2<i32>(load_i32(), load_next_i32());
                 // yyyyxxxx, yyyyxxxx, wwwwzzzz, wwwwzzzz
-                auto* xxyy = ctx.dst->MemberAccessor(i32s, "xxyy");
+                auto* xxyy = b.MemberAccessor(i32s, "xxyy");
                 // xxxx0000, yyyyxxxx, zzzz0000, wwwwzzzz
-                auto* shl = ctx.dst->Shl(xxyy, ctx.dst->vec4<u32>(16_u, 0_u, 16_u, 0_u));
+                auto* shl = b.Shl(xxyy, b.vec4<u32>(16_u, 0_u, 16_u, 0_u));
                 // ssssxxxx, ssssyyyy, sssszzzz, sssswwww
-                return ctx.dst->Shr(shl, ctx.dst->vec4<u32>(16_u));
+                return b.Shr(shl, b.vec4<u32>(16_u));
             }
             case VertexFormat::kUnorm8x2:
-                return ctx.dst->MemberAccessor(ctx.dst->Call("unpack4x8unorm", load_u16_l()), "xy");
+                return b.MemberAccessor(b.Call("unpack4x8unorm", load_u16_l()), "xy");
             case VertexFormat::kSnorm8x2:
-                return ctx.dst->MemberAccessor(ctx.dst->Call("unpack4x8snorm", load_u16_l()), "xy");
+                return b.MemberAccessor(b.Call("unpack4x8snorm", load_u16_l()), "xy");
             case VertexFormat::kUnorm8x4:
-                return ctx.dst->Call("unpack4x8unorm", load_u32());
+                return b.Call("unpack4x8unorm", load_u32());
             case VertexFormat::kSnorm8x4:
-                return ctx.dst->Call("unpack4x8snorm", load_u32());
+                return b.Call("unpack4x8snorm", load_u32());
             case VertexFormat::kUnorm16x2:
-                return ctx.dst->Call("unpack2x16unorm", load_u32());
+                return b.Call("unpack2x16unorm", load_u32());
             case VertexFormat::kSnorm16x2:
-                return ctx.dst->Call("unpack2x16snorm", load_u32());
+                return b.Call("unpack2x16snorm", load_u32());
             case VertexFormat::kFloat16x2:
-                return ctx.dst->Call("unpack2x16float", load_u32());
+                return b.Call("unpack2x16float", load_u32());
             case VertexFormat::kUnorm16x4:
-                return ctx.dst->vec4<f32>(ctx.dst->Call("unpack2x16unorm", load_u32()),
-                                          ctx.dst->Call("unpack2x16unorm", load_next_u32()));
+                return b.vec4<f32>(b.Call("unpack2x16unorm", load_u32()),
+                                   b.Call("unpack2x16unorm", load_next_u32()));
             case VertexFormat::kSnorm16x4:
-                return ctx.dst->vec4<f32>(ctx.dst->Call("unpack2x16snorm", load_u32()),
-                                          ctx.dst->Call("unpack2x16snorm", load_next_u32()));
+                return b.vec4<f32>(b.Call("unpack2x16snorm", load_u32()),
+                                   b.Call("unpack2x16snorm", load_next_u32()));
             case VertexFormat::kFloat16x4:
-                return ctx.dst->vec4<f32>(ctx.dst->Call("unpack2x16float", load_u32()),
-                                          ctx.dst->Call("unpack2x16float", load_next_u32()));
+                return b.vec4<f32>(b.Call("unpack2x16float", load_u32()),
+                                   b.Call("unpack2x16float", load_next_u32()));
         }
 
-        TINT_UNREACHABLE(Transform, ctx.dst->Diagnostics())
-            << "format " << static_cast<int>(format);
+        TINT_UNREACHABLE(Transform, b.Diagnostics()) << "format " << static_cast<int>(format);
         return nullptr;
     }
 
@@ -623,12 +656,12 @@
 
             const ast ::Expression* index = nullptr;
             if (offset > 0) {
-                index = ctx.dst->Add(array_base, u32(offset / 4));
+                index = b.Add(array_base, u32(offset / 4));
             } else {
-                index = ctx.dst->Expr(array_base);
+                index = b.Expr(array_base);
             }
-            u = ctx.dst->IndexAccessor(
-                ctx.dst->MemberAccessor(GetVertexBufferName(buffer), GetStructBufferName()), index);
+            u = b.IndexAccessor(
+                b.MemberAccessor(GetVertexBufferName(buffer), GetStructBufferName()), index);
 
         } else {
             // Unaligned load
@@ -639,22 +672,22 @@
 
             uint32_t shift = 8u * (offset & 3u);
 
-            auto* low_shr = ctx.dst->Shr(low, u32(shift));
-            auto* high_shl = ctx.dst->Shl(high, u32(32u - shift));
-            u = ctx.dst->Or(low_shr, high_shl);
+            auto* low_shr = b.Shr(low, u32(shift));
+            auto* high_shl = b.Shl(high, u32(32u - shift));
+            u = b.Or(low_shr, high_shl);
         }
 
         switch (format) {
             case VertexFormat::kUint32:
                 return u;
             case VertexFormat::kSint32:
-                return ctx.dst->Bitcast(ctx.dst->ty.i32(), u);
+                return b.Bitcast(b.ty.i32(), u);
             case VertexFormat::kFloat32:
-                return ctx.dst->Bitcast(ctx.dst->ty.f32(), u);
+                return b.Bitcast(b.ty.f32(), u);
             default:
                 break;
         }
-        TINT_UNREACHABLE(Transform, ctx.dst->Diagnostics())
+        TINT_UNREACHABLE(Transform, b.Diagnostics())
             << "invalid format for LoadPrimitive" << static_cast<int>(format);
         return nullptr;
     }
@@ -682,8 +715,7 @@
             expr_list.Push(LoadPrimitive(array_base, primitive_offset, buffer, base_format));
         }
 
-        return ctx.dst->Construct(ctx.dst->create<ast::Vector>(base_type, count),
-                                  std::move(expr_list));
+        return b.Construct(b.create<ast::Vector>(base_type, count), std::move(expr_list));
     }
 
     /// Process a non-struct entry point parameter.
@@ -696,34 +728,30 @@
             // Create a function-scope variable to replace the parameter.
             auto func_var_sym = ctx.Clone(param->symbol);
             auto* func_var_type = ctx.Clone(param->type);
-            auto* func_var = ctx.dst->Var(func_var_sym, func_var_type);
-            ctx.InsertFront(func->body->statements, ctx.dst->Decl(func_var));
+            auto* func_var = b.Var(func_var_sym, func_var_type);
+            ctx.InsertFront(func->body->statements, b.Decl(func_var));
             // Capture mapping from location to the new variable.
             LocationInfo info;
-            info.expr = [this, func_var]() { return ctx.dst->Expr(func_var); };
+            info.expr = [this, func_var]() { return b.Expr(func_var); };
 
-            auto* sem = ctx.src->Sem().Get<sem::Parameter>(param);
+            auto* sem = src->Sem().Get<sem::Parameter>(param);
             info.type = sem->Type();
 
             if (!sem->Location().has_value()) {
-                TINT_ICE(Transform, ctx.dst->Diagnostics()) << "Location missing value";
+                TINT_ICE(Transform, b.Diagnostics()) << "Location missing value";
                 return;
             }
             location_info[sem->Location().value()] = info;
         } else if (auto* builtin = ast::GetAttribute<ast::BuiltinAttribute>(param->attributes)) {
             // Check for existing vertex_index and instance_index builtins.
             if (builtin->builtin == ast::BuiltinValue::kVertexIndex) {
-                vertex_index_expr = [this, param]() {
-                    return ctx.dst->Expr(ctx.Clone(param->symbol));
-                };
+                vertex_index_expr = [this, param]() { return b.Expr(ctx.Clone(param->symbol)); };
             } else if (builtin->builtin == ast::BuiltinValue::kInstanceIndex) {
-                instance_index_expr = [this, param]() {
-                    return ctx.dst->Expr(ctx.Clone(param->symbol));
-                };
+                instance_index_expr = [this, param]() { return b.Expr(ctx.Clone(param->symbol)); };
             }
             new_function_parameters.Push(ctx.Clone(param));
         } else {
-            TINT_ICE(Transform, ctx.dst->Diagnostics()) << "Invalid entry point parameter";
+            TINT_ICE(Transform, b.Diagnostics()) << "Invalid entry point parameter";
         }
     }
 
@@ -746,7 +774,7 @@
         for (auto* member : struct_ty->members) {
             auto member_sym = ctx.Clone(member->symbol);
             std::function<const ast::Expression*()> member_expr = [this, param_sym, member_sym]() {
-                return ctx.dst->MemberAccessor(param_sym, member_sym);
+                return b.MemberAccessor(param_sym, member_sym);
             };
 
             if (ast::HasAttribute<ast::LocationAttribute>(member->attributes)) {
@@ -754,7 +782,7 @@
                 LocationInfo info;
                 info.expr = member_expr;
 
-                auto* sem = ctx.src->Sem().Get(member);
+                auto* sem = src->Sem().Get(member);
                 info.type = sem->Type();
 
                 TINT_ASSERT(Transform, sem->Location().has_value());
@@ -770,7 +798,7 @@
                 }
                 members_to_clone.Push(member);
             } else {
-                TINT_ICE(Transform, ctx.dst->Diagnostics()) << "Invalid entry point parameter";
+                TINT_ICE(Transform, b.Diagnostics()) << "Invalid entry point parameter";
             }
         }
 
@@ -781,8 +809,8 @@
         }
 
         // Create a function-scope variable to replace the parameter.
-        auto* func_var = ctx.dst->Var(param_sym, ctx.Clone(param->type));
-        ctx.InsertFront(func->body->statements, ctx.dst->Decl(func_var));
+        auto* func_var = b.Var(param_sym, ctx.Clone(param->type));
+        ctx.InsertFront(func->body->statements, b.Decl(func_var));
 
         if (!members_to_clone.IsEmpty()) {
             // Create a new struct without the location attributes.
@@ -791,20 +819,20 @@
                 auto member_sym = ctx.Clone(member->symbol);
                 auto* member_type = ctx.Clone(member->type);
                 auto member_attrs = ctx.Clone(member->attributes);
-                new_members.Push(ctx.dst->Member(member_sym, member_type, std::move(member_attrs)));
+                new_members.Push(b.Member(member_sym, member_type, std::move(member_attrs)));
             }
-            auto* new_struct = ctx.dst->Structure(ctx.dst->Sym(), new_members);
+            auto* new_struct = b.Structure(b.Sym(), new_members);
 
             // Create a new function parameter with this struct.
-            auto* new_param = ctx.dst->Param(ctx.dst->Sym(), ctx.dst->ty.Of(new_struct));
+            auto* new_param = b.Param(b.Sym(), b.ty.Of(new_struct));
             new_function_parameters.Push(new_param);
 
             // Copy values from the new parameter to the function-scope variable.
             for (auto* member : members_to_clone) {
                 auto member_name = ctx.Clone(member->symbol);
                 ctx.InsertFront(func->body->statements,
-                                ctx.dst->Assign(ctx.dst->MemberAccessor(func_var, member_name),
-                                                ctx.dst->MemberAccessor(new_param, member_name)));
+                                b.Assign(b.MemberAccessor(func_var, member_name),
+                                         b.MemberAccessor(new_param, member_name)));
             }
         }
     }
@@ -818,7 +846,7 @@
 
         // Process entry point parameters.
         for (auto* param : func->params) {
-            auto* sem = ctx.src->Sem().Get(param);
+            auto* sem = src->Sem().Get(param);
             if (auto* str = sem->Type()->As<sem::Struct>()) {
                 ProcessStructParameter(func, param, str->Declaration());
             } else {
@@ -830,11 +858,11 @@
         if (!vertex_index_expr) {
             for (const VertexBufferLayoutDescriptor& layout : cfg.vertex_state) {
                 if (layout.step_mode == VertexStepMode::kVertex) {
-                    auto name = ctx.dst->Symbols().New("tint_pulling_vertex_index");
-                    new_function_parameters.Push(ctx.dst->Param(
-                        name, ctx.dst->ty.u32(),
-                        utils::Vector{ctx.dst->Builtin(ast::BuiltinValue::kVertexIndex)}));
-                    vertex_index_expr = [this, name]() { return ctx.dst->Expr(name); };
+                    auto name = b.Symbols().New("tint_pulling_vertex_index");
+                    new_function_parameters.Push(
+                        b.Param(name, b.ty.u32(),
+                                utils::Vector{b.Builtin(ast::BuiltinValue::kVertexIndex)}));
+                    vertex_index_expr = [this, name]() { return b.Expr(name); };
                     break;
                 }
             }
@@ -842,11 +870,11 @@
         if (!instance_index_expr) {
             for (const VertexBufferLayoutDescriptor& layout : cfg.vertex_state) {
                 if (layout.step_mode == VertexStepMode::kInstance) {
-                    auto name = ctx.dst->Symbols().New("tint_pulling_instance_index");
-                    new_function_parameters.Push(ctx.dst->Param(
-                        name, ctx.dst->ty.u32(),
-                        utils::Vector{ctx.dst->Builtin(ast::BuiltinValue::kInstanceIndex)}));
-                    instance_index_expr = [this, name]() { return ctx.dst->Expr(name); };
+                    auto name = b.Symbols().New("tint_pulling_instance_index");
+                    new_function_parameters.Push(
+                        b.Param(name, b.ty.u32(),
+                                utils::Vector{b.Builtin(ast::BuiltinValue::kInstanceIndex)}));
+                    instance_index_expr = [this, name]() { return b.Expr(name); };
                     break;
                 }
             }
@@ -864,53 +892,24 @@
         auto attrs = ctx.Clone(func->attributes);
         auto ret_attrs = ctx.Clone(func->return_type_attributes);
         auto* new_func =
-            ctx.dst->create<ast::Function>(func->source, func_sym, new_function_parameters,
-                                           ret_type, body, std::move(attrs), std::move(ret_attrs));
+            b.create<ast::Function>(func->source, func_sym, new_function_parameters, ret_type, body,
+                                    std::move(attrs), std::move(ret_attrs));
         ctx.Replace(func, new_func);
     }
 };
 
-}  // namespace
-
 VertexPulling::VertexPulling() = default;
 VertexPulling::~VertexPulling() = default;
 
-void VertexPulling::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) const {
+Transform::ApplyResult VertexPulling::Apply(const Program* src,
+                                            const DataMap& inputs,
+                                            DataMap&) const {
     auto cfg = cfg_;
     if (auto* cfg_data = inputs.Get<Config>()) {
         cfg = *cfg_data;
     }
 
-    // Find entry point
-    const ast::Function* func = nullptr;
-    for (auto* fn : ctx.src->AST().Functions()) {
-        if (fn->PipelineStage() == ast::PipelineStage::kVertex) {
-            if (func != nullptr) {
-                ctx.dst->Diagnostics().add_error(
-                    diag::System::Transform,
-                    "VertexPulling found more than one vertex entry point");
-                return;
-            }
-            func = fn;
-        }
-    }
-    if (func == nullptr) {
-        ctx.dst->Diagnostics().add_error(diag::System::Transform,
-                                         "Vertex stage entry point not found");
-        return;
-    }
-
-    // TODO(idanr): Need to check shader locations in descriptor cover all
-    // attributes
-
-    // TODO(idanr): Make sure we covered all error cases, to guarantee the
-    // following stages will pass
-
-    State state{ctx, cfg};
-    state.AddVertexStorageBuffers();
-    state.Process(func);
-
-    ctx.Clone();
+    return State{src, cfg}.Run();
 }
 
 VertexPulling::Config::Config() = default;
diff --git a/src/tint/transform/vertex_pulling.h b/src/tint/transform/vertex_pulling.h
index 6dd35bc..c0f88a5 100644
--- a/src/tint/transform/vertex_pulling.h
+++ b/src/tint/transform/vertex_pulling.h
@@ -171,16 +171,14 @@
     /// Destructor
     ~VertexPulling() override;
 
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
   private:
+    struct State;
+
     Config cfg_;
 };
 
diff --git a/src/tint/transform/while_to_loop.cc b/src/tint/transform/while_to_loop.cc
index 45944e6..d359d2e 100644
--- a/src/tint/transform/while_to_loop.cc
+++ b/src/tint/transform/while_to_loop.cc
@@ -14,18 +14,17 @@
 
 #include "src/tint/transform/while_to_loop.h"
 
+#include <utility>
+
 #include "src/tint/ast/break_statement.h"
 #include "src/tint/program_builder.h"
 
 TINT_INSTANTIATE_TYPEINFO(tint::transform::WhileToLoop);
 
 namespace tint::transform {
+namespace {
 
-WhileToLoop::WhileToLoop() = default;
-
-WhileToLoop::~WhileToLoop() = default;
-
-bool WhileToLoop::ShouldRun(const Program* program, const DataMap&) const {
+bool ShouldRun(const Program* program) {
     for (auto* node : program->ASTNodes().Objects()) {
         if (node->Is<ast::WhileStatement>()) {
             return true;
@@ -34,20 +33,32 @@
     return false;
 }
 
-void WhileToLoop::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
+}  // namespace
+
+WhileToLoop::WhileToLoop() = default;
+
+WhileToLoop::~WhileToLoop() = default;
+
+Transform::ApplyResult WhileToLoop::Apply(const Program* src, const DataMap&, DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
+    }
+
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
     ctx.ReplaceAll([&](const ast::WhileStatement* w) -> const ast::Statement* {
         utils::Vector<const ast::Statement*, 16> stmts;
         auto* cond = w->condition;
 
         // !condition
-        auto* not_cond =
-            ctx.dst->create<ast::UnaryOpExpression>(ast::UnaryOp::kNot, ctx.Clone(cond));
+        auto* not_cond = b.Not(ctx.Clone(cond));
 
         // { break; }
-        auto* break_body = ctx.dst->Block(ctx.dst->create<ast::BreakStatement>());
+        auto* break_body = b.Block(b.Break());
 
         // if (!condition) { break; }
-        stmts.Push(ctx.dst->If(not_cond, break_body));
+        stmts.Push(b.If(not_cond, break_body));
 
         for (auto* stmt : w->body->statements) {
             stmts.Push(ctx.Clone(stmt));
@@ -55,13 +66,14 @@
 
         const ast::BlockStatement* continuing = nullptr;
 
-        auto* body = ctx.dst->Block(stmts);
-        auto* loop = ctx.dst->create<ast::LoopStatement>(body, continuing);
+        auto* body = b.Block(stmts);
+        auto* loop = b.Loop(body, continuing);
 
         return loop;
     });
 
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/while_to_loop.h b/src/tint/transform/while_to_loop.h
index 4915d68..187799a 100644
--- a/src/tint/transform/while_to_loop.h
+++ b/src/tint/transform/while_to_loop.h
@@ -29,19 +29,10 @@
     /// Destructor
     ~WhileToLoop() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 };
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/zero_init_workgroup_memory.cc b/src/tint/transform/zero_init_workgroup_memory.cc
index ea65436..ed3584e9 100644
--- a/src/tint/transform/zero_init_workgroup_memory.cc
+++ b/src/tint/transform/zero_init_workgroup_memory.cc
@@ -31,10 +31,24 @@
 TINT_INSTANTIATE_TYPEINFO(tint::transform::ZeroInitWorkgroupMemory);
 
 namespace tint::transform {
+namespace {
+
+bool ShouldRun(const Program* program) {
+    for (auto* global : program->AST().GlobalVariables()) {
+        if (auto* var = global->As<ast::Var>()) {
+            if (var->declared_address_space == ast::AddressSpace::kWorkgroup) {
+                return true;
+            }
+        }
+    }
+    return false;
+}
+
+}  // namespace
 
 using StatementList = utils::Vector<const ast::Statement*, 8>;
 
-/// PIMPL state for the ZeroInitWorkgroupMemory transform
+/// PIMPL state for the transform
 struct ZeroInitWorkgroupMemory::State {
     /// The clone context
     CloneContext& ctx;
@@ -424,24 +438,24 @@
 
 ZeroInitWorkgroupMemory::~ZeroInitWorkgroupMemory() = default;
 
-bool ZeroInitWorkgroupMemory::ShouldRun(const Program* program, const DataMap&) const {
-    for (auto* global : program->AST().GlobalVariables()) {
-        if (auto* var = global->As<ast::Var>()) {
-            if (var->declared_address_space == ast::AddressSpace::kWorkgroup) {
-                return true;
-            }
-        }
+Transform::ApplyResult ZeroInitWorkgroupMemory::Apply(const Program* src,
+                                                      const DataMap&,
+                                                      DataMap&) const {
+    if (!ShouldRun(src)) {
+        return SkipTransform;
     }
-    return false;
-}
 
-void ZeroInitWorkgroupMemory::Run(CloneContext& ctx, const DataMap&, DataMap&) const {
-    for (auto* fn : ctx.src->AST().Functions()) {
+    ProgramBuilder b;
+    CloneContext ctx{&b, src, /* auto_clone_symbols */ true};
+
+    for (auto* fn : src->AST().Functions()) {
         if (fn->PipelineStage() == ast::PipelineStage::kCompute) {
             State{ctx}.Run(fn);
         }
     }
+
     ctx.Clone();
+    return Program(std::move(b));
 }
 
 }  // namespace tint::transform
diff --git a/src/tint/transform/zero_init_workgroup_memory.h b/src/tint/transform/zero_init_workgroup_memory.h
index 07feaa8..64f4da8 100644
--- a/src/tint/transform/zero_init_workgroup_memory.h
+++ b/src/tint/transform/zero_init_workgroup_memory.h
@@ -30,19 +30,10 @@
     /// Destructor
     ~ZeroInitWorkgroupMemory() override;
 
-    /// @param program the program to inspect
-    /// @param data optional extra transform-specific input data
-    /// @returns true if this transform should be run for the given program
-    bool ShouldRun(const Program* program, const DataMap& data = {}) const override;
-
-  protected:
-    /// Runs the transform using the CloneContext built for transforming a
-    /// program. Run() is responsible for calling Clone() on the CloneContext.
-    /// @param ctx the CloneContext primed with the input program and
-    /// ProgramBuilder
-    /// @param inputs optional extra transform-specific input data
-    /// @param outputs optional extra transform-specific output data
-    void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs) const override;
+    /// @copydoc Transform::Apply
+    ApplyResult Apply(const Program* program,
+                      const DataMap& inputs,
+                      DataMap& outputs) const override;
 
   private:
     struct State;
diff --git a/test/tint/bug/tint/1739.wgsl.expected.dxc.hlsl b/test/tint/bug/tint/1739.wgsl.expected.dxc.hlsl
index 6a6f107..a80ef5b 100644
--- a/test/tint/bug/tint/1739.wgsl.expected.dxc.hlsl
+++ b/test/tint/bug/tint/1739.wgsl.expected.dxc.hlsl
@@ -1,3 +1,7 @@
+int2 tint_clamp(int2 e, int2 low, int2 high) {
+  return min(max(e, low), high);
+}
+
 struct GammaTransferParams {
   float G;
   float A;
@@ -46,10 +50,6 @@
   return float4(color, 1.0f);
 }
 
-int2 tint_clamp(int2 e, int2 low, int2 high) {
-  return min(max(e, low), high);
-}
-
 float3x4 tint_symbol_6(uint4 buffer[11], uint offset) {
   const uint scalar_offset = ((offset + 0u)) / 4;
   const uint scalar_offset_1 = ((offset + 16u)) / 4;
diff --git a/test/tint/bug/tint/1739.wgsl.expected.fxc.hlsl b/test/tint/bug/tint/1739.wgsl.expected.fxc.hlsl
index 6a6f107..a80ef5b 100644
--- a/test/tint/bug/tint/1739.wgsl.expected.fxc.hlsl
+++ b/test/tint/bug/tint/1739.wgsl.expected.fxc.hlsl
@@ -1,3 +1,7 @@
+int2 tint_clamp(int2 e, int2 low, int2 high) {
+  return min(max(e, low), high);
+}
+
 struct GammaTransferParams {
   float G;
   float A;
@@ -46,10 +50,6 @@
   return float4(color, 1.0f);
 }
 
-int2 tint_clamp(int2 e, int2 low, int2 high) {
-  return min(max(e, low), high);
-}
-
 float3x4 tint_symbol_6(uint4 buffer[11], uint offset) {
   const uint scalar_offset = ((offset + 0u)) / 4;
   const uint scalar_offset_1 = ((offset + 16u)) / 4;
diff --git a/test/tint/bug/tint/1739.wgsl.expected.msl b/test/tint/bug/tint/1739.wgsl.expected.msl
index e1802c5..ed7a995 100644
--- a/test/tint/bug/tint/1739.wgsl.expected.msl
+++ b/test/tint/bug/tint/1739.wgsl.expected.msl
@@ -14,6 +14,10 @@
     T elements[N];
 };
 
+int2 tint_clamp(int2 e, int2 low, int2 high) {
+  return min(max(e, low), high);
+}
+
 struct GammaTransferParams {
   /* 0x0000 */ float G;
   /* 0x0004 */ float A;
@@ -57,10 +61,6 @@
   return float4(color, 1.0f);
 }
 
-int2 tint_clamp(int2 e, int2 low, int2 high) {
-  return min(max(e, low), high);
-}
-
 kernel void tint_symbol(texture2d<float, access::sample> tint_symbol_5 [[texture(0)]], texture2d<float, access::sample> tint_symbol_6 [[texture(1)]], const constant ExternalTextureParams* tint_symbol_7 [[buffer(0)]], texture2d<float, access::write> tint_symbol_8 [[texture(2)]]) {
   int2 const tint_symbol_1 = tint_clamp(int2(10), int2(0), int2((uint2(uint2(tint_symbol_5.get_width(), tint_symbol_5.get_height())) - uint2(1u))));
   float4 red = textureLoadExternal(tint_symbol_5, tint_symbol_6, tint_symbol_1, *(tint_symbol_7));
diff --git a/test/tint/bug/tint/1739.wgsl.expected.spvasm b/test/tint/bug/tint/1739.wgsl.expected.spvasm
index 2cdbccb..2f01aa5 100644
--- a/test/tint/bug/tint/1739.wgsl.expected.spvasm
+++ b/test/tint/bug/tint/1739.wgsl.expected.spvasm
@@ -5,7 +5,7 @@
 ; Schema: 0
                OpCapability Shader
                OpCapability ImageQuery
-         %25 = OpExtInstImport "GLSL.std.450"
+         %28 = OpExtInstImport "GLSL.std.450"
                OpMemoryModel Logical GLSL450
                OpEntryPoint GLCompute %main "main"
                OpExecutionMode %main LocalSize 1 1 1
@@ -31,6 +31,10 @@
                OpName %ext_tex_params "ext_tex_params"
                OpName %t "t"
                OpName %outImage "outImage"
+               OpName %tint_clamp "tint_clamp"
+               OpName %e "e"
+               OpName %low "low"
+               OpName %high "high"
                OpName %gammaCorrection "gammaCorrection"
                OpName %v "v"
                OpName %params "params"
@@ -40,10 +44,6 @@
                OpName %coord "coord"
                OpName %params_0 "params"
                OpName %color "color"
-               OpName %tint_clamp "tint_clamp"
-               OpName %e "e"
-               OpName %low "low"
-               OpName %high "high"
                OpName %main "main"
                OpName %red "red"
                OpName %green "green"
@@ -95,20 +95,20 @@
          %18 = OpTypeImage %float 2D 0 0 0 2 Rgba8
 %_ptr_UniformConstant_18 = OpTypePointer UniformConstant %18
    %outImage = OpVariable %_ptr_UniformConstant_18 UniformConstant
-         %19 = OpTypeFunction %v3float %v3float %GammaTransferParams
+        %int = OpTypeInt 32 1
+      %v2int = OpTypeVector %int 2
+         %19 = OpTypeFunction %v2int %v2int %v2int %v2int
+         %30 = OpTypeFunction %v3float %v3float %GammaTransferParams
        %bool = OpTypeBool
      %v3bool = OpTypeVector %bool 3
 %_ptr_Function_v3float = OpTypePointer Function %v3float
-         %39 = OpConstantNull %v3float
-        %int = OpTypeInt 32 1
-      %v2int = OpTypeVector %int 2
-         %59 = OpTypeFunction %v4float %3 %3 %v2int %ExternalTextureParams
+         %49 = OpConstantNull %v3float
+         %69 = OpTypeFunction %v4float %3 %3 %v2int %ExternalTextureParams
      %uint_1 = OpConstant %uint 1
-         %76 = OpConstantNull %int
+         %84 = OpConstantNull %int
     %v2float = OpTypeVector %float 2
     %float_1 = OpConstant %float 1
-         %90 = OpConstantNull %uint
-        %108 = OpTypeFunction %v2int %v2int %v2int %v2int
+         %98 = OpConstantNull %uint
        %void = OpTypeVoid
         %116 = OpTypeFunction %void
      %int_10 = OpConstant %int 10
@@ -125,106 +125,106 @@
     %int_118 = OpConstant %int 118
         %154 = OpConstantComposite %v2int %int_70 %int_118
       %int_1 = OpConstant %int 1
-        %168 = OpConstantComposite %v2int %int_1 %76
-%gammaCorrection = OpFunction %v3float None %19
+        %168 = OpConstantComposite %v2int %int_1 %84
+ %tint_clamp = OpFunction %v2int None %19
+          %e = OpFunctionParameter %v2int
+        %low = OpFunctionParameter %v2int
+       %high = OpFunctionParameter %v2int
+         %26 = OpLabel
+         %29 = OpExtInst %v2int %28 SMax %e %low
+         %27 = OpExtInst %v2int %28 SMin %29 %high
+               OpReturnValue %27
+               OpFunctionEnd
+%gammaCorrection = OpFunction %v3float None %30
           %v = OpFunctionParameter %v3float
      %params = OpFunctionParameter %GammaTransferParams
-         %23 = OpLabel
-         %37 = OpVariable %_ptr_Function_v3float Function %39
-         %49 = OpVariable %_ptr_Function_v3float Function %39
-         %55 = OpVariable %_ptr_Function_v3float Function %39
-         %24 = OpExtInst %v3float %25 FAbs %v
-         %26 = OpCompositeExtract %float %params 4
-         %27 = OpCompositeConstruct %v3float %26 %26 %26
-         %28 = OpFOrdLessThan %v3bool %24 %27
-         %31 = OpExtInst %v3float %25 FSign %v
-         %32 = OpCompositeExtract %float %params 3
-         %33 = OpExtInst %v3float %25 FAbs %v
-         %34 = OpVectorTimesScalar %v3float %33 %32
-         %35 = OpCompositeExtract %float %params 6
-         %40 = OpCompositeConstruct %v3float %35 %35 %35
-         %36 = OpFAdd %v3float %34 %40
-         %41 = OpFMul %v3float %31 %36
-         %42 = OpExtInst %v3float %25 FSign %v
-         %44 = OpCompositeExtract %float %params 1
-         %45 = OpExtInst %v3float %25 FAbs %v
-         %46 = OpVectorTimesScalar %v3float %45 %44
-         %47 = OpCompositeExtract %float %params 2
-         %50 = OpCompositeConstruct %v3float %47 %47 %47
-         %48 = OpFAdd %v3float %46 %50
-         %51 = OpCompositeExtract %float %params 0
-         %52 = OpCompositeConstruct %v3float %51 %51 %51
-         %43 = OpExtInst %v3float %25 Pow %48 %52
-         %53 = OpCompositeExtract %float %params 5
-         %56 = OpCompositeConstruct %v3float %53 %53 %53
-         %54 = OpFAdd %v3float %43 %56
-         %57 = OpFMul %v3float %42 %54
-         %58 = OpSelect %v3float %28 %41 %57
-               OpReturnValue %58
+         %34 = OpLabel
+         %47 = OpVariable %_ptr_Function_v3float Function %49
+         %59 = OpVariable %_ptr_Function_v3float Function %49
+         %65 = OpVariable %_ptr_Function_v3float Function %49
+         %35 = OpExtInst %v3float %28 FAbs %v
+         %36 = OpCompositeExtract %float %params 4
+         %37 = OpCompositeConstruct %v3float %36 %36 %36
+         %38 = OpFOrdLessThan %v3bool %35 %37
+         %41 = OpExtInst %v3float %28 FSign %v
+         %42 = OpCompositeExtract %float %params 3
+         %43 = OpExtInst %v3float %28 FAbs %v
+         %44 = OpVectorTimesScalar %v3float %43 %42
+         %45 = OpCompositeExtract %float %params 6
+         %50 = OpCompositeConstruct %v3float %45 %45 %45
+         %46 = OpFAdd %v3float %44 %50
+         %51 = OpFMul %v3float %41 %46
+         %52 = OpExtInst %v3float %28 FSign %v
+         %54 = OpCompositeExtract %float %params 1
+         %55 = OpExtInst %v3float %28 FAbs %v
+         %56 = OpVectorTimesScalar %v3float %55 %54
+         %57 = OpCompositeExtract %float %params 2
+         %60 = OpCompositeConstruct %v3float %57 %57 %57
+         %58 = OpFAdd %v3float %56 %60
+         %61 = OpCompositeExtract %float %params 0
+         %62 = OpCompositeConstruct %v3float %61 %61 %61
+         %53 = OpExtInst %v3float %28 Pow %58 %62
+         %63 = OpCompositeExtract %float %params 5
+         %66 = OpCompositeConstruct %v3float %63 %63 %63
+         %64 = OpFAdd %v3float %53 %66
+         %67 = OpFMul %v3float %52 %64
+         %68 = OpSelect %v3float %38 %51 %67
+               OpReturnValue %68
                OpFunctionEnd
-%textureLoadExternal = OpFunction %v4float None %59
+%textureLoadExternal = OpFunction %v4float None %69
      %plane0 = OpFunctionParameter %3
      %plane1 = OpFunctionParameter %3
       %coord = OpFunctionParameter %v2int
    %params_0 = OpFunctionParameter %ExternalTextureParams
-         %67 = OpLabel
-      %color = OpVariable %_ptr_Function_v3float Function %39
-         %69 = OpCompositeExtract %uint %params_0 0
-         %71 = OpIEqual %bool %69 %uint_1
-               OpSelectionMerge %72 None
-               OpBranchConditional %71 %73 %74
-         %73 = OpLabel
-         %75 = OpImageFetch %v4float %plane0 %coord Lod %76
-         %77 = OpVectorShuffle %v3float %75 %75 0 1 2
-               OpStore %color %77
-               OpBranch %72
-         %74 = OpLabel
-         %78 = OpImageFetch %v4float %plane0 %coord Lod %76
-         %79 = OpCompositeExtract %float %78 0
-         %80 = OpImageFetch %v4float %plane1 %coord Lod %76
-         %82 = OpVectorShuffle %v2float %80 %80 0 1
-         %83 = OpCompositeExtract %float %82 0
-         %84 = OpCompositeExtract %float %82 1
-         %86 = OpCompositeConstruct %v4float %79 %83 %84 %float_1
-         %87 = OpCompositeExtract %mat3v4float %params_0 2
-         %88 = OpVectorTimesMatrix %v3float %86 %87
-               OpStore %color %88
-               OpBranch %72
-         %72 = OpLabel
-         %89 = OpCompositeExtract %uint %params_0 1
-         %91 = OpIEqual %bool %89 %90
-               OpSelectionMerge %92 None
-               OpBranchConditional %91 %93 %92
-         %93 = OpLabel
-         %95 = OpLoad %v3float %color
-         %96 = OpCompositeExtract %GammaTransferParams %params_0 3
-         %94 = OpFunctionCall %v3float %gammaCorrection %95 %96
-               OpStore %color %94
-         %97 = OpCompositeExtract %mat3v3float %params_0 5
-         %98 = OpLoad %v3float %color
-         %99 = OpMatrixTimesVector %v3float %97 %98
-               OpStore %color %99
-        %101 = OpLoad %v3float %color
-        %102 = OpCompositeExtract %GammaTransferParams %params_0 4
-        %100 = OpFunctionCall %v3float %gammaCorrection %101 %102
-               OpStore %color %100
-               OpBranch %92
-         %92 = OpLabel
+         %75 = OpLabel
+      %color = OpVariable %_ptr_Function_v3float Function %49
+         %77 = OpCompositeExtract %uint %params_0 0
+         %79 = OpIEqual %bool %77 %uint_1
+               OpSelectionMerge %80 None
+               OpBranchConditional %79 %81 %82
+         %81 = OpLabel
+         %83 = OpImageFetch %v4float %plane0 %coord Lod %84
+         %85 = OpVectorShuffle %v3float %83 %83 0 1 2
+               OpStore %color %85
+               OpBranch %80
+         %82 = OpLabel
+         %86 = OpImageFetch %v4float %plane0 %coord Lod %84
+         %87 = OpCompositeExtract %float %86 0
+         %88 = OpImageFetch %v4float %plane1 %coord Lod %84
+         %90 = OpVectorShuffle %v2float %88 %88 0 1
+         %91 = OpCompositeExtract %float %90 0
+         %92 = OpCompositeExtract %float %90 1
+         %94 = OpCompositeConstruct %v4float %87 %91 %92 %float_1
+         %95 = OpCompositeExtract %mat3v4float %params_0 2
+         %96 = OpVectorTimesMatrix %v3float %94 %95
+               OpStore %color %96
+               OpBranch %80
+         %80 = OpLabel
+         %97 = OpCompositeExtract %uint %params_0 1
+         %99 = OpIEqual %bool %97 %98
+               OpSelectionMerge %100 None
+               OpBranchConditional %99 %101 %100
+        %101 = OpLabel
         %103 = OpLoad %v3float %color
-        %104 = OpCompositeExtract %float %103 0
-        %105 = OpCompositeExtract %float %103 1
-        %106 = OpCompositeExtract %float %103 2
-        %107 = OpCompositeConstruct %v4float %104 %105 %106 %float_1
-               OpReturnValue %107
-               OpFunctionEnd
- %tint_clamp = OpFunction %v2int None %108
-          %e = OpFunctionParameter %v2int
-        %low = OpFunctionParameter %v2int
-       %high = OpFunctionParameter %v2int
-        %113 = OpLabel
-        %115 = OpExtInst %v2int %25 SMax %e %low
-        %114 = OpExtInst %v2int %25 SMin %115 %high
-               OpReturnValue %114
+        %104 = OpCompositeExtract %GammaTransferParams %params_0 3
+        %102 = OpFunctionCall %v3float %gammaCorrection %103 %104
+               OpStore %color %102
+        %105 = OpCompositeExtract %mat3v3float %params_0 5
+        %106 = OpLoad %v3float %color
+        %107 = OpMatrixTimesVector %v3float %105 %106
+               OpStore %color %107
+        %109 = OpLoad %v3float %color
+        %110 = OpCompositeExtract %GammaTransferParams %params_0 4
+        %108 = OpFunctionCall %v3float %gammaCorrection %109 %110
+               OpStore %color %108
+               OpBranch %100
+        %100 = OpLabel
+        %111 = OpLoad %v3float %color
+        %112 = OpCompositeExtract %float %111 0
+        %113 = OpCompositeExtract %float %111 1
+        %114 = OpCompositeExtract %float %111 2
+        %115 = OpCompositeConstruct %v4float %112 %113 %114 %float_1
+               OpReturnValue %115
                OpFunctionEnd
        %main = OpFunction %void None %116
         %119 = OpLabel
diff --git a/test/tint/builtins/gen/literal/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.dxc.hlsl b/test/tint/builtins/gen/literal/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.dxc.hlsl
index c1df2b1..2799157 100644
--- a/test/tint/builtins/gen/literal/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.dxc.hlsl
+++ b/test/tint/builtins/gen/literal/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.dxc.hlsl
@@ -1,6 +1,3 @@
-Texture2D<float4> arg_0 : register(t0, space1);
-SamplerState arg_1 : register(s1, space1);
-
 float4 tint_textureSampleBaseClampToEdge(Texture2D<float4> t, SamplerState s, float2 coord) {
   int3 tint_tmp;
   t.GetDimensions(0, tint_tmp.x, tint_tmp.y, tint_tmp.z);
@@ -10,6 +7,9 @@
   return t.SampleLevel(s, clamped, 0.0f);
 }
 
+Texture2D<float4> arg_0 : register(t0, space1);
+SamplerState arg_1 : register(s1, space1);
+
 void textureSampleBaseClampToEdge_9ca02c() {
   float4 res = tint_textureSampleBaseClampToEdge(arg_0, arg_1, (0.0f).xx);
 }
diff --git a/test/tint/builtins/gen/literal/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.fxc.hlsl b/test/tint/builtins/gen/literal/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.fxc.hlsl
index c1df2b1..2799157 100644
--- a/test/tint/builtins/gen/literal/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.fxc.hlsl
+++ b/test/tint/builtins/gen/literal/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.fxc.hlsl
@@ -1,6 +1,3 @@
-Texture2D<float4> arg_0 : register(t0, space1);
-SamplerState arg_1 : register(s1, space1);
-
 float4 tint_textureSampleBaseClampToEdge(Texture2D<float4> t, SamplerState s, float2 coord) {
   int3 tint_tmp;
   t.GetDimensions(0, tint_tmp.x, tint_tmp.y, tint_tmp.z);
@@ -10,6 +7,9 @@
   return t.SampleLevel(s, clamped, 0.0f);
 }
 
+Texture2D<float4> arg_0 : register(t0, space1);
+SamplerState arg_1 : register(s1, space1);
+
 void textureSampleBaseClampToEdge_9ca02c() {
   float4 res = tint_textureSampleBaseClampToEdge(arg_0, arg_1, (0.0f).xx);
 }
diff --git a/test/tint/builtins/gen/var/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.dxc.hlsl b/test/tint/builtins/gen/var/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.dxc.hlsl
index 870d5d4..1e3e8bd 100644
--- a/test/tint/builtins/gen/var/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.dxc.hlsl
+++ b/test/tint/builtins/gen/var/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.dxc.hlsl
@@ -1,6 +1,3 @@
-Texture2D<float4> arg_0 : register(t0, space1);
-SamplerState arg_1 : register(s1, space1);
-
 float4 tint_textureSampleBaseClampToEdge(Texture2D<float4> t, SamplerState s, float2 coord) {
   int3 tint_tmp;
   t.GetDimensions(0, tint_tmp.x, tint_tmp.y, tint_tmp.z);
@@ -10,6 +7,9 @@
   return t.SampleLevel(s, clamped, 0.0f);
 }
 
+Texture2D<float4> arg_0 : register(t0, space1);
+SamplerState arg_1 : register(s1, space1);
+
 void textureSampleBaseClampToEdge_9ca02c() {
   float2 arg_2 = (0.0f).xx;
   float4 res = tint_textureSampleBaseClampToEdge(arg_0, arg_1, arg_2);
diff --git a/test/tint/builtins/gen/var/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.fxc.hlsl b/test/tint/builtins/gen/var/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.fxc.hlsl
index 870d5d4..1e3e8bd 100644
--- a/test/tint/builtins/gen/var/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.fxc.hlsl
+++ b/test/tint/builtins/gen/var/textureSampleBaseClampToEdge/9ca02c.wgsl.expected.fxc.hlsl
@@ -1,6 +1,3 @@
-Texture2D<float4> arg_0 : register(t0, space1);
-SamplerState arg_1 : register(s1, space1);
-
 float4 tint_textureSampleBaseClampToEdge(Texture2D<float4> t, SamplerState s, float2 coord) {
   int3 tint_tmp;
   t.GetDimensions(0, tint_tmp.x, tint_tmp.y, tint_tmp.z);
@@ -10,6 +7,9 @@
   return t.SampleLevel(s, clamped, 0.0f);
 }
 
+Texture2D<float4> arg_0 : register(t0, space1);
+SamplerState arg_1 : register(s1, space1);
+
 void textureSampleBaseClampToEdge_9ca02c() {
   float2 arg_2 = (0.0f).xx;
   float4 res = tint_textureSampleBaseClampToEdge(arg_0, arg_1, arg_2);