diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 98699d6..8352f9e 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -860,7 +860,7 @@
 
   if(${TINT_BUILD_WGSL_READER} AND ${TINT_BUILD_WGSL_WRITER})
     list(APPEND TINT_TEST_SRCS
-      transform/array_length_from_uniform.cc
+      transform/array_length_from_uniform_test.cc
       transform/binding_remapper_test.cc
       transform/bound_array_accessors_test.cc
       transform/calculate_array_length_test.cc
diff --git a/src/clone_context.cc b/src/clone_context.cc
index 16fc90b..993431e 100644
--- a/src/clone_context.cc
+++ b/src/clone_context.cc
@@ -57,6 +57,7 @@
 
 void CloneContext::Clone() {
   dst->AST().Copy(this, &src->AST());
+  dst->SetTransformApplied(src->TransformsApplied());
 }
 
 ast::FunctionList CloneContext::Clone(const ast::FunctionList& v) {
diff --git a/src/program.cc b/src/program.cc
index 81c24f0..24d2a1f 100644
--- a/src/program.cc
+++ b/src/program.cc
@@ -33,6 +33,7 @@
       sem_(std::move(program.sem_)),
       symbols_(std::move(program.symbols_)),
       diagnostics_(std::move(program.diagnostics_)),
+      transforms_applied_(std::move(program.transforms_applied_)),
       is_valid_(program.is_valid_) {
   program.AssertNotMoved();
   program.moved_ = true;
@@ -57,6 +58,7 @@
   sem_ = std::move(builder.Sem());
   symbols_ = std::move(builder.Symbols());
   diagnostics_.add(std::move(builder.Diagnostics()));
+  transforms_applied_ = builder.TransformsApplied();
   builder.MarkAsMoved();
 
   if (!is_valid_ && !diagnostics_.contains_errors()) {
@@ -80,6 +82,7 @@
   sem_ = std::move(program.sem_);
   symbols_ = std::move(program.symbols_);
   diagnostics_ = std::move(program.diagnostics_);
+  transforms_applied_ = std::move(program.transforms_applied_);
   is_valid_ = program.is_valid_;
   return *this;
 }
diff --git a/src/program.h b/src/program.h
index d2c5f82..32534fa 100644
--- a/src/program.h
+++ b/src/program.h
@@ -16,6 +16,7 @@
 #define SRC_PROGRAM_H_
 
 #include <string>
+#include <unordered_set>
 
 #include "src/ast/function.h"
 #include "src/program_id.h"
@@ -125,6 +126,25 @@
   /// information
   bool IsValid() const;
 
+  /// @return the TypeInfo pointers of all transforms that have been applied to
+  /// this program.
+  std::unordered_set<const TypeInfo*> TransformsApplied() const {
+    return transforms_applied_;
+  }
+
+  /// @param transform the TypeInfo of the transform
+  /// @returns true if the transform with the given TypeInfo was applied to the
+  /// Program
+  bool HasTransformApplied(const TypeInfo* transform) const {
+    return transforms_applied_.count(transform);
+  }
+
+  /// @returns true if the transform of type `T` was applied.
+  template <typename T>
+  bool HasTransformApplied() const {
+    return HasTransformApplied(&TypeInfo::Of<T>());
+  }
+
   /// Helper for returning the resolved semantic type of the expression `expr`.
   /// @param expr the AST expression
   /// @return the resolved semantic type for the expression, or nullptr if the
@@ -180,6 +200,7 @@
   sem::Info sem_;
   SymbolTable symbols_{id_};
   diag::List diagnostics_;
+  std::unordered_set<const TypeInfo*> transforms_applied_;
   bool is_valid_ = false;  // Not valid until it is built
   bool moved_ = false;
 };
diff --git a/src/program_builder.cc b/src/program_builder.cc
index effe513..fb82ec6 100644
--- a/src/program_builder.cc
+++ b/src/program_builder.cc
@@ -37,7 +37,9 @@
       sem_nodes_(std::move(rhs.sem_nodes_)),
       ast_(rhs.ast_),
       sem_(std::move(rhs.sem_)),
-      symbols_(std::move(rhs.symbols_)) {
+      symbols_(std::move(rhs.symbols_)),
+      diagnostics_(std::move(rhs.diagnostics_)),
+      transforms_applied_(std::move(rhs.transforms_applied_)) {
   rhs.MarkAsMoved();
 }
 
@@ -53,6 +55,8 @@
   ast_ = rhs.ast_;
   sem_ = std::move(rhs.sem_);
   symbols_ = std::move(rhs.symbols_);
+  diagnostics_ = std::move(rhs.diagnostics_);
+  transforms_applied_ = std::move(rhs.transforms_applied_);
   return *this;
 }
 
@@ -65,6 +69,7 @@
   builder.sem_ = sem::Info::Wrap(program->Sem());
   builder.symbols_ = program->Symbols();
   builder.diagnostics_ = program->Diagnostics();
+  builder.transforms_applied_ = program->TransformsApplied();
   return builder;
 }
 
diff --git a/src/program_builder.h b/src/program_builder.h
index bf03e0a..facd539 100644
--- a/src/program_builder.h
+++ b/src/program_builder.h
@@ -16,6 +16,7 @@
 #define SRC_PROGRAM_BUILDER_H_
 
 #include <string>
+#include <unordered_set>
 #include <utility>
 
 #include "src/ast/alias.h"
@@ -84,13 +85,14 @@
 #error "internal tint header being #included from tint.h"
 #endif
 
-namespace tint {
-
 // Forward declarations
+namespace tint {
 namespace ast {
 class VariableDeclStatement;
 }  // namespace ast
+}  // namespace tint
 
+namespace tint {
 class CloneContext;
 
 /// ProgramBuilder is a mutable builder for a Program.
@@ -2039,6 +2041,40 @@
     source_ = Source(loc);
   }
 
+  /// Marks that the given transform has been applied to this program.
+  /// @param transform the transform that has been applied
+  void SetTransformApplied(const CastableBase* transform) {
+    transforms_applied_.emplace(&transform->TypeInfo());
+  }
+
+  /// Marks that the given transform `T` has been applied to this program.
+  template <typename T>
+  void SetTransformApplied() {
+    transforms_applied_.emplace(&TypeInfo::Of<T>());
+  }
+
+  /// Marks that the transforms with the given TypeInfos have been applied to
+  /// this program.
+  /// @param transforms the set of transform TypeInfos that has been applied
+  void SetTransformApplied(
+      const std::unordered_set<const TypeInfo*>& transforms) {
+    for (auto* transform : transforms) {
+      transforms_applied_.emplace(transform);
+    }
+  }
+
+  /// @returns true if the transform of type `T` was applied.
+  template <typename T>
+  bool HasTransformApplied() {
+    return transforms_applied_.count(&TypeInfo::Of<T>());
+  }
+
+  /// @return the TypeInfo pointers of all transforms that have been applied to
+  /// this program.
+  std::unordered_set<const TypeInfo*> TransformsApplied() const {
+    return transforms_applied_;
+  }
+
   /// Helper for returning the resolved semantic type of the expression `expr`.
   /// @note As the Resolver is run when the Program is built, this will only be
   /// useful for the Resolver itself and tests that use their own Resolver.
@@ -2125,6 +2161,7 @@
   sem::Info sem_;
   SymbolTable symbols_{id_};
   diag::List diagnostics_;
+  std::unordered_set<const TypeInfo*> transforms_applied_;
 
   /// The source to use when creating AST nodes without providing a Source as
   /// the first argument.
diff --git a/src/transform/array_length_from_uniform.cc b/src/transform/array_length_from_uniform.cc
index e7fa0f7..9cd1096 100644
--- a/src/transform/array_length_from_uniform.cc
+++ b/src/transform/array_length_from_uniform.cc
@@ -21,7 +21,10 @@
 #include "src/program_builder.h"
 #include "src/sem/call.h"
 #include "src/sem/variable.h"
+#include "src/transform/inline_pointer_lets.h"
+#include "src/transform/simplify.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::ArrayLengthFromUniform);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::ArrayLengthFromUniform::Config);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::ArrayLengthFromUniform::Result);
 
@@ -31,16 +34,19 @@
 ArrayLengthFromUniform::ArrayLengthFromUniform() = default;
 ArrayLengthFromUniform::~ArrayLengthFromUniform() = default;
 
-Output ArrayLengthFromUniform::Run(const Program* in, const DataMap& data) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
+void ArrayLengthFromUniform::Run(CloneContext& ctx,
+                                 const DataMap& inputs,
+                                 DataMap& outputs) {
+  if (!Requires<InlinePointerLets, Simplify>(ctx)) {
+    return;
+  }
 
-  auto* cfg = data.Get<Config>();
+  auto* cfg = inputs.Get<Config>();
   if (cfg == nullptr) {
-    out.Diagnostics().add_error(
+    ctx.dst->Diagnostics().add_error(
         diag::System::Transform,
         "missing transform data for ArrayLengthFromUniform");
-    return Output(Program(std::move(out)));
+    return;
   }
 
   auto& sem = ctx.src->Sem();
@@ -149,8 +155,7 @@
 
   ctx.Clone();
 
-  return Output{Program(std::move(out)),
-                std::make_unique<Result>(buffer_size_ubo ? true : false)};
+  outputs.Add<Result>(buffer_size_ubo ? true : false);
 }
 
 ArrayLengthFromUniform::Config::Config(sem::BindingPoint ubo_bp)
diff --git a/src/transform/array_length_from_uniform.h b/src/transform/array_length_from_uniform.h
index 7ccb588..a310616 100644
--- a/src/transform/array_length_from_uniform.h
+++ b/src/transform/array_length_from_uniform.h
@@ -49,7 +49,8 @@
 /// This transform assumes that the `InlinePointerLets` and `Simplify`
 /// transforms have been run before it so that arguments to the arrayLength
 /// builtin always have the form `&resource.array`.
-class ArrayLengthFromUniform : public Transform {
+class ArrayLengthFromUniform
+    : public Castable<ArrayLengthFromUniform, Transform> {
  public:
   /// Constructor
   ArrayLengthFromUniform();
@@ -91,11 +92,14 @@
     bool const needs_buffer_sizes;
   };
 
-  /// 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/array_length_from_uniform_test.cc b/src/transform/array_length_from_uniform_test.cc
index 006e094..808e4a7 100644
--- a/src/transform/array_length_from_uniform_test.cc
+++ b/src/transform/array_length_from_uniform_test.cc
@@ -16,6 +16,8 @@
 
 #include <utility>
 
+#include "src/transform/inline_pointer_lets.h"
+#include "src/transform/simplify.h"
 #include "src/transform/test_helper.h"
 
 namespace tint {
@@ -29,7 +31,31 @@
 
   auto* expect = "error: missing transform data for ArrayLengthFromUniform";
 
-  auto got = Run<ArrayLengthFromUniform>(src);
+  auto got = Run<InlinePointerLets, Simplify, ArrayLengthFromUniform>(src);
+
+  EXPECT_EQ(expect, str(got));
+}
+
+TEST_F(ArrayLengthFromUniformTest, Error_MissingInlinePointerLets) {
+  auto* src = "";
+
+  auto* expect =
+      "error: tint::transform::ArrayLengthFromUniform depends on "
+      "tint::transform::InlinePointerLets but the dependency was not run";
+
+  auto got = Run<Simplify, ArrayLengthFromUniform>(src);
+
+  EXPECT_EQ(expect, str(got));
+}
+
+TEST_F(ArrayLengthFromUniformTest, Error_MissingSimplify) {
+  auto* src = "";
+
+  auto* expect =
+      "error: tint::transform::ArrayLengthFromUniform depends on "
+      "tint::transform::Simplify but the dependency was not run";
+
+  auto got = Run<InlinePointerLets, ArrayLengthFromUniform>(src);
 
   EXPECT_EQ(expect, str(got));
 }
@@ -78,7 +104,8 @@
   DataMap data;
   data.Add<ArrayLengthFromUniform::Config>(std::move(cfg));
 
-  auto got = Run<ArrayLengthFromUniform>(src, data);
+  auto got =
+      Run<InlinePointerLets, Simplify, ArrayLengthFromUniform>(src, data);
 
   EXPECT_EQ(expect, str(got));
   EXPECT_TRUE(
@@ -131,7 +158,8 @@
   DataMap data;
   data.Add<ArrayLengthFromUniform::Config>(std::move(cfg));
 
-  auto got = Run<ArrayLengthFromUniform>(src, data);
+  auto got =
+      Run<InlinePointerLets, Simplify, ArrayLengthFromUniform>(src, data);
 
   EXPECT_EQ(expect, str(got));
   EXPECT_TRUE(
@@ -203,7 +231,8 @@
   DataMap data;
   data.Add<ArrayLengthFromUniform::Config>(std::move(cfg));
 
-  auto got = Run<ArrayLengthFromUniform>(src, data);
+  auto got =
+      Run<InlinePointerLets, Simplify, ArrayLengthFromUniform>(src, data);
 
   EXPECT_EQ(expect, str(got));
   EXPECT_TRUE(
@@ -232,7 +261,8 @@
   DataMap data;
   data.Add<ArrayLengthFromUniform::Config>(std::move(cfg));
 
-  auto got = Run<ArrayLengthFromUniform>(src, data);
+  auto got =
+      Run<InlinePointerLets, Simplify, ArrayLengthFromUniform>(src, data);
 
   EXPECT_EQ(src, str(got));
   EXPECT_FALSE(
@@ -273,7 +303,8 @@
   DataMap data;
   data.Add<ArrayLengthFromUniform::Config>(std::move(cfg));
 
-  auto got = Run<ArrayLengthFromUniform>(src, data);
+  auto got =
+      Run<InlinePointerLets, Simplify, ArrayLengthFromUniform>(src, data);
 
   EXPECT_EQ(expect, str(got));
 }
diff --git a/src/transform/binding_remapper.cc b/src/transform/binding_remapper.cc
index 5873cfe..5e6cc20 100644
--- a/src/transform/binding_remapper.cc
+++ b/src/transform/binding_remapper.cc
@@ -22,6 +22,7 @@
 #include "src/sem/function.h"
 #include "src/sem/variable.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::BindingRemapper);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::BindingRemapper::Remappings);
 
 namespace tint {
@@ -40,14 +41,13 @@
 BindingRemapper::BindingRemapper() = default;
 BindingRemapper::~BindingRemapper() = default;
 
-Output BindingRemapper::Run(const Program* in, const DataMap& datamap) {
-  ProgramBuilder out;
-  auto* remappings = datamap.Get<Remappings>();
+void BindingRemapper::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) {
+  auto* remappings = inputs.Get<Remappings>();
   if (!remappings) {
-    out.Diagnostics().add_error(
+    ctx.dst->Diagnostics().add_error(
         diag::System::Transform,
         "BindingRemapper did not find the remapping data");
-    return Output(Program(std::move(out)));
+    return;
   }
 
   // A set of post-remapped binding points that need to be decorated with a
@@ -57,11 +57,11 @@
   if (remappings->allow_collisions) {
     // Scan for binding point collisions generated by this transform.
     // Populate all collisions in the `add_collision_deco` set.
-    for (auto* func_ast : in->AST().Functions()) {
+    for (auto* func_ast : ctx.src->AST().Functions()) {
       if (!func_ast->IsEntryPoint()) {
         continue;
       }
-      auto* func = in->Sem().Get(func_ast);
+      auto* func = ctx.src->Sem().Get(func_ast);
       std::unordered_map<sem::BindingPoint, int> binding_point_counts;
       for (auto* var : func->ReferencedModuleVariables()) {
         if (auto binding_point = var->Declaration()->binding_point()) {
@@ -85,9 +85,7 @@
     }
   }
 
-  CloneContext ctx(&out, in);
-
-  for (auto* var : in->AST().GlobalVariables()) {
+  for (auto* var : ctx.src->AST().GlobalVariables()) {
     if (auto binding_point = var->binding_point()) {
       // The original binding point
       BindingPoint from{binding_point.group->value(),
@@ -102,8 +100,8 @@
       auto bp_it = remappings->binding_points.find(from);
       if (bp_it != remappings->binding_points.end()) {
         BindingPoint to = bp_it->second;
-        auto* new_group = out.create<ast::GroupDecoration>(to.group);
-        auto* new_binding = out.create<ast::BindingDecoration>(to.binding);
+        auto* new_group = ctx.dst->create<ast::GroupDecoration>(to.group);
+        auto* new_binding = ctx.dst->create<ast::BindingDecoration>(to.binding);
 
         ctx.Replace(binding_point.group, new_group);
         ctx.Replace(binding_point.binding, new_binding);
@@ -114,7 +112,7 @@
       auto ac_it = remappings->access_controls.find(from);
       if (ac_it != remappings->access_controls.end()) {
         ast::Access ac = ac_it->second;
-        auto* ty = in->Sem().Get(var)->Type()->UnwrapRef();
+        auto* ty = ctx.src->Sem().Get(var)->Type()->UnwrapRef();
         ast::Type* inner_ty = CreateASTTypeFor(&ctx, ty);
         auto* new_var = ctx.dst->create<ast::Variable>(
             ctx.Clone(var->source()), ctx.Clone(var->symbol()),
@@ -133,8 +131,8 @@
       }
     }
   }
+
   ctx.Clone();
-  return Output(Program(std::move(out)));
 }
 
 }  // namespace transform
diff --git a/src/transform/binding_remapper.h b/src/transform/binding_remapper.h
index b271c1f..5fd2fc8 100644
--- a/src/transform/binding_remapper.h
+++ b/src/transform/binding_remapper.h
@@ -29,7 +29,7 @@
 
 /// BindingRemapper is a transform used to remap resource binding points and
 /// access controls.
-class BindingRemapper : public Transform {
+class BindingRemapper : public Castable<BindingRemapper, Transform> {
  public:
   /// BindingPoints is a map of old binding point to new binding point
   using BindingPoints = std::unordered_map<BindingPoint, BindingPoint>;
@@ -68,11 +68,14 @@
   BindingRemapper();
   ~BindingRemapper() 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/bound_array_accessors.cc b/src/transform/bound_array_accessors.cc
index e2b1860..5ad5020 100644
--- a/src/transform/bound_array_accessors.cc
+++ b/src/transform/bound_array_accessors.cc
@@ -20,20 +20,20 @@
 #include "src/program_builder.h"
 #include "src/sem/expression.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::BoundArrayAccessors);
+
 namespace tint {
 namespace transform {
 
 BoundArrayAccessors::BoundArrayAccessors() = default;
 BoundArrayAccessors::~BoundArrayAccessors() = default;
 
-Output BoundArrayAccessors::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
+void BoundArrayAccessors::Run(CloneContext& ctx, const DataMap&, DataMap&) {
   ctx.ReplaceAll([&](ast::ArrayAccessorExpression* expr) {
     return Transform(expr, &ctx);
   });
+
   ctx.Clone();
-  return Output(Program(std::move(out)));
 }
 
 ast::ArrayAccessorExpression* BoundArrayAccessors::Transform(
diff --git a/src/transform/bound_array_accessors.h b/src/transform/bound_array_accessors.h
index c2330ad..87803e6 100644
--- a/src/transform/bound_array_accessors.h
+++ b/src/transform/bound_array_accessors.h
@@ -25,18 +25,21 @@
 /// the bounds of the array. Any access before the start of the array will clamp
 /// to zero and any access past the end of the array will clamp to
 /// (array length - 1).
-class BoundArrayAccessors : public Transform {
+class BoundArrayAccessors : public Castable<BoundArrayAccessors, Transform> {
  public:
   /// Constructor
   BoundArrayAccessors();
   /// Destructor
   ~BoundArrayAccessors() 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 = {}) 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) override;
 
  private:
   ast::ArrayAccessorExpression* Transform(ast::ArrayAccessorExpression* expr,
diff --git a/src/transform/calculate_array_length.cc b/src/transform/calculate_array_length.cc
index ee48611..0983818 100644
--- a/src/transform/calculate_array_length.cc
+++ b/src/transform/calculate_array_length.cc
@@ -27,6 +27,7 @@
 #include "src/utils/get_or_create.h"
 #include "src/utils/hash.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::CalculateArrayLength);
 TINT_INSTANTIATE_TYPEINFO(
     tint::transform::CalculateArrayLength::BufferSizeIntrinsic);
 
@@ -69,10 +70,7 @@
 CalculateArrayLength::CalculateArrayLength() = default;
 CalculateArrayLength::~CalculateArrayLength() = default;
 
-Output CalculateArrayLength::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
+void CalculateArrayLength::Run(CloneContext& ctx, const DataMap&, DataMap&) {
   auto& sem = ctx.src->Sem();
 
   // get_buffer_size_intrinsic() emits the function decorated with
@@ -232,8 +230,6 @@
   }
 
   ctx.Clone();
-
-  return Output{Program(std::move(out))};
 }
 
 }  // namespace transform
diff --git a/src/transform/calculate_array_length.h b/src/transform/calculate_array_length.h
index ba0279a..2003058 100644
--- a/src/transform/calculate_array_length.h
+++ b/src/transform/calculate_array_length.h
@@ -29,7 +29,7 @@
 
 /// CalculateArrayLength is a transform used to replace calls to arrayLength()
 /// with a value calculated from the size of the storage buffer.
-class CalculateArrayLength : public Transform {
+class CalculateArrayLength : public Castable<CalculateArrayLength, Transform> {
  public:
   /// BufferSizeIntrinsic is an InternalDecoration that's applied to intrinsic
   /// functions used to obtain the runtime size of a storage buffer.
@@ -56,11 +56,14 @@
   /// Destructor
   ~CalculateArrayLength() override;
 
-  /// 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/canonicalize_entry_point_io.cc b/src/transform/canonicalize_entry_point_io.cc
index eaf9ce9..34ef071 100644
--- a/src/transform/canonicalize_entry_point_io.cc
+++ b/src/transform/canonicalize_entry_point_io.cc
@@ -24,6 +24,7 @@
 #include "src/sem/struct.h"
 #include "src/sem/variable.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::CanonicalizeEntryPointIO);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::CanonicalizeEntryPointIO::Config);
 
 namespace tint {
@@ -62,16 +63,15 @@
 
 }  // namespace
 
-Output CanonicalizeEntryPointIO::Run(const Program* in, const DataMap& data) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
-  auto* cfg = data.Get<Config>();
+void CanonicalizeEntryPointIO::Run(CloneContext& ctx,
+                                   const DataMap& inputs,
+                                   DataMap&) {
+  auto* cfg = inputs.Get<Config>();
   if (cfg == nullptr) {
-    out.Diagnostics().add_error(
+    ctx.dst->Diagnostics().add_error(
         diag::System::Transform,
         "missing transform data for CanonicalizeEntryPointIO");
-    return Output(Program(std::move(out)));
+    return;
   }
 
   // Strip entry point IO decorations from struct declarations.
@@ -375,7 +375,6 @@
   }
 
   ctx.Clone();
-  return Output(Program(std::move(out)));
 }
 
 CanonicalizeEntryPointIO::Config::Config(BuiltinStyle builtins,
diff --git a/src/transform/canonicalize_entry_point_io.h b/src/transform/canonicalize_entry_point_io.h
index a7f3465..5d9a47b 100644
--- a/src/transform/canonicalize_entry_point_io.h
+++ b/src/transform/canonicalize_entry_point_io.h
@@ -68,7 +68,8 @@
 ///   return retval;
 /// }
 /// ```
-class CanonicalizeEntryPointIO : public Transform {
+class CanonicalizeEntryPointIO
+    : public Castable<CanonicalizeEntryPointIO, Transform> {
  public:
   /// BuiltinStyle is an enumerator of different ways to emit builtins.
   enum class BuiltinStyle {
@@ -102,11 +103,14 @@
   CanonicalizeEntryPointIO();
   ~CanonicalizeEntryPointIO() 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/decompose_memory_access.cc b/src/transform/decompose_memory_access.cc
index 96a373a..7f81894 100644
--- a/src/transform/decompose_memory_access.cc
+++ b/src/transform/decompose_memory_access.cc
@@ -38,6 +38,7 @@
 #include "src/utils/get_or_create.h"
 #include "src/utils/hash.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::DecomposeMemoryAccess);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::DecomposeMemoryAccess::Intrinsic);
 
 namespace tint {
@@ -790,10 +791,7 @@
 DecomposeMemoryAccess::DecomposeMemoryAccess() = default;
 DecomposeMemoryAccess::~DecomposeMemoryAccess() = default;
 
-Output DecomposeMemoryAccess::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
+void DecomposeMemoryAccess::Run(CloneContext& ctx, const DataMap&, DataMap&) {
   auto& sem = ctx.src->Sem();
 
   State state;
@@ -987,7 +985,6 @@
   }
 
   ctx.Clone();
-  return Output{Program(std::move(out))};
 }
 
 }  // namespace transform
diff --git a/src/transform/decompose_memory_access.h b/src/transform/decompose_memory_access.h
index c65a5fe..d1cadad 100644
--- a/src/transform/decompose_memory_access.h
+++ b/src/transform/decompose_memory_access.h
@@ -30,7 +30,8 @@
 /// DecomposeMemoryAccess is a transform used to replace storage and uniform
 /// buffer accesses with a combination of load, store or atomic functions on
 /// primitive types.
-class DecomposeMemoryAccess : public Transform {
+class DecomposeMemoryAccess
+    : public Castable<DecomposeMemoryAccess, Transform> {
  public:
   /// Intrinsic is an InternalDecoration that's used to decorate a stub function
   /// so that the HLSL transforms this into calls to
@@ -103,11 +104,14 @@
   /// Destructor
   ~DecomposeMemoryAccess() override;
 
-  /// 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 = {}) 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) override;
 
   struct State;
 };
diff --git a/src/transform/external_texture_transform.cc b/src/transform/external_texture_transform.cc
index 4d48ff7..1ede9b8 100644
--- a/src/transform/external_texture_transform.cc
+++ b/src/transform/external_texture_transform.cc
@@ -18,15 +18,17 @@
 #include "src/sem/call.h"
 #include "src/sem/variable.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::ExternalTextureTransform);
+
 namespace tint {
 namespace transform {
 
 ExternalTextureTransform::ExternalTextureTransform() = default;
 ExternalTextureTransform::~ExternalTextureTransform() = default;
 
-Output ExternalTextureTransform::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
+void ExternalTextureTransform::Run(CloneContext& ctx,
+                                   const DataMap&,
+                                   DataMap&) {
   auto& sem = ctx.src->Sem();
 
   // Within this transform, usages of texture_external are replaced with a
@@ -105,7 +107,7 @@
   // Scan the AST nodes for external texture declarations.
   for (auto* node : ctx.src->ASTNodes().Objects()) {
     if (auto* var = node->As<ast::Variable>()) {
-      if (Is<ast::ExternalTexture>(var->type())) {
+      if (::tint::Is<ast::ExternalTexture>(var->type())) {
         // Replace a single-plane external texture with a 2D, f32 sampled
         // texture.
         auto* newType = ctx.dst->ty.sampled_texture(ast::TextureDimension::k2d,
@@ -125,7 +127,6 @@
   }
 
   ctx.Clone();
-  return Output{Program(std::move(out))};
 }
 
 }  // namespace transform
diff --git a/src/transform/external_texture_transform.h b/src/transform/external_texture_transform.h
index 350122b..6bb8091 100644
--- a/src/transform/external_texture_transform.h
+++ b/src/transform/external_texture_transform.h
@@ -27,18 +27,22 @@
 /// This allows us to share SPIR-V/HLSL writer paths for sampled textures
 /// instead of adding dedicated writer paths for external textures.
 /// ExternalTextureTransform performs this transformation.
-class ExternalTextureTransform : public Transform {
+class ExternalTextureTransform
+    : public Castable<ExternalTextureTransform, Transform> {
  public:
   /// Constructor
   ExternalTextureTransform();
   /// Destructor
   ~ExternalTextureTransform() override;
 
-  /// 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/first_index_offset.cc b/src/transform/first_index_offset.cc
index 4a69c63..8a28364 100644
--- a/src/transform/first_index_offset.cc
+++ b/src/transform/first_index_offset.cc
@@ -25,6 +25,7 @@
 #include "src/sem/struct.h"
 #include "src/sem/variable.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::FirstIndexOffset);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::FirstIndexOffset::BindingPoint);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::FirstIndexOffset::Data);
 
@@ -57,18 +58,17 @@
 FirstIndexOffset::FirstIndexOffset() = default;
 FirstIndexOffset::~FirstIndexOffset() = default;
 
-Output FirstIndexOffset::Run(const Program* in, const DataMap& data) {
+void FirstIndexOffset::Run(CloneContext& ctx,
+                           const DataMap& inputs,
+                           DataMap& outputs) {
   // Get the uniform buffer binding point
   uint32_t ub_binding = binding_;
   uint32_t ub_group = group_;
-  if (auto* binding_point = data.Get<BindingPoint>()) {
+  if (auto* binding_point = inputs.Get<BindingPoint>()) {
     ub_binding = binding_point->binding;
     ub_group = binding_point->group;
   }
 
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
   // Map of builtin usages
   std::unordered_map<const sem::Variable*, const char*> builtin_vars;
   std::unordered_map<const sem::StructMember*, const char*> builtin_members;
@@ -78,7 +78,7 @@
 
   // Traverse the AST scanning for builtin accesses via variables (includes
   // parameters) or structure member accesses.
-  for (auto* node : in->ASTNodes().Objects()) {
+  for (auto* node : ctx.src->ASTNodes().Objects()) {
     if (auto* var = node->As<ast::Variable>()) {
       for (ast::Decoration* dec : var->decorations()) {
         if (auto* builtin_dec = dec->As<ast::BuiltinDecoration>()) {
@@ -173,10 +173,8 @@
 
   ctx.Clone();
 
-  return Output(
-      Program(std::move(out)),
-      std::make_unique<Data>(has_vertex_index, has_instance_index,
-                             vertex_index_offset, instance_index_offset));
+  outputs.Add<Data>(has_vertex_index, has_instance_index, vertex_index_offset,
+                    instance_index_offset);
 }
 
 }  // namespace transform
diff --git a/src/transform/first_index_offset.h b/src/transform/first_index_offset.h
index f84e9e3..2ba27b5 100644
--- a/src/transform/first_index_offset.h
+++ b/src/transform/first_index_offset.h
@@ -55,7 +55,7 @@
 ///     return vert_idx;
 ///   }
 ///
-class FirstIndexOffset : public Transform {
+class FirstIndexOffset : public Castable<FirstIndexOffset, Transform> {
  public:
   /// BindingPoint is consumed by the FirstIndexOffset transform.
   /// BindingPoint specifies the binding point of the first index uniform
@@ -112,11 +112,14 @@
   /// Destructor
   ~FirstIndexOffset() 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 = {}) 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) override;
 
  private:
   uint32_t binding_ = 0;
diff --git a/src/transform/fold_constants.cc b/src/transform/fold_constants.cc
index 3fe3691..6fcc798 100644
--- a/src/transform/fold_constants.cc
+++ b/src/transform/fold_constants.cc
@@ -20,6 +20,8 @@
 
 #include "src/program_builder.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::FoldConstants);
+
 namespace tint {
 
 namespace {
@@ -318,10 +320,7 @@
 
 FoldConstants::~FoldConstants() = default;
 
-Output FoldConstants::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
+void FoldConstants::Run(CloneContext& ctx, const DataMap&, DataMap&) {
   ExprToValue expr_to_value;
 
   // Visit inner expressions before outer expressions
@@ -345,8 +344,6 @@
   }
 
   ctx.Clone();
-
-  return Output(Program(std::move(out)));
 }
 
 }  // namespace transform
diff --git a/src/transform/fold_constants.h b/src/transform/fold_constants.h
index 7e18337..861a06b 100644
--- a/src/transform/fold_constants.h
+++ b/src/transform/fold_constants.h
@@ -21,7 +21,7 @@
 namespace transform {
 
 /// FoldConstants transforms the AST by folding constant expressions
-class FoldConstants : public Transform {
+class FoldConstants : public Castable<FoldConstants, Transform> {
  public:
   /// Constructor
   FoldConstants();
@@ -29,11 +29,14 @@
   /// Destructor
   ~FoldConstants() 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/hlsl.cc b/src/transform/hlsl.cc
index 1009f05..cca668f 100644
--- a/src/transform/hlsl.cc
+++ b/src/transform/hlsl.cc
@@ -29,6 +29,8 @@
 #include "src/transform/wrap_arrays_in_structs.h"
 #include "src/transform/zero_init_workgroup_memory.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::Hlsl);
+
 namespace tint {
 namespace transform {
 
@@ -69,6 +71,7 @@
   CloneContext ctx(&builder, &out.program);
   AddEmptyEntryPoint(ctx);
   ctx.Clone();
+  builder.SetTransformApplied(this);
   return Output{Program(std::move(builder))};
 }
 
diff --git a/src/transform/hlsl.h b/src/transform/hlsl.h
index 9cffd77..091903e 100644
--- a/src/transform/hlsl.h
+++ b/src/transform/hlsl.h
@@ -27,7 +27,7 @@
 /// Hlsl is a transform used to sanitize a Program for use with the Hlsl writer.
 /// Passing a non-sanitized Program to the Hlsl writer will result in undefined
 /// behavior.
-class Hlsl : public Transform {
+class Hlsl : public Castable<Hlsl, Transform> {
  public:
   /// Constructor
   Hlsl();
diff --git a/src/transform/inline_pointer_lets.cc b/src/transform/inline_pointer_lets.cc
index b82d730..6b18f75 100644
--- a/src/transform/inline_pointer_lets.cc
+++ b/src/transform/inline_pointer_lets.cc
@@ -25,6 +25,8 @@
 #include "src/sem/variable.h"
 #include "src/utils/scoped_assignment.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::InlinePointerLets);
+
 namespace tint {
 namespace transform {
 namespace {
@@ -79,10 +81,7 @@
 
 InlinePointerLets::~InlinePointerLets() = default;
 
-Output InlinePointerLets::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
+void InlinePointerLets::Run(CloneContext& ctx, const DataMap&, DataMap&) {
   // If not null, current_ptr_let is the current PtrLet being operated on.
   PtrLet* current_ptr_let = nullptr;
   // A map of the AST `let` variable to the PtrLet
@@ -107,7 +106,7 @@
       }
     }
     if (auto* ident = expr->As<ast::IdentifierExpression>()) {
-      if (auto* vu = in->Sem().Get<sem::VariableUser>(ident)) {
+      if (auto* vu = ctx.src->Sem().Get<sem::VariableUser>(ident)) {
         auto* var = vu->Variable()->Declaration();
         auto it = ptr_lets.find(var);
         if (it != ptr_lets.end()) {
@@ -130,13 +129,13 @@
   // Find all the pointer-typed `let` declarations.
   // Note that these must be function-scoped, as module-scoped `let`s are not
   // permitted.
-  for (auto* node : in->ASTNodes().Objects()) {
+  for (auto* node : ctx.src->ASTNodes().Objects()) {
     if (auto* let = node->As<ast::VariableDeclStatement>()) {
       if (!let->variable()->is_const()) {
         continue;  // Not a `let` declaration. Ignore.
       }
 
-      auto* var = in->Sem().Get(let->variable());
+      auto* var = ctx.src->Sem().Get(let->variable());
       if (!var->Type()->Is<sem::Pointer>()) {
         continue;  // Not a pointer type. Ignore.
       }
@@ -183,8 +182,6 @@
   }
 
   ctx.Clone();
-
-  return Output(Program(std::move(out)));
 }
 
 }  // namespace transform
diff --git a/src/transform/inline_pointer_lets.h b/src/transform/inline_pointer_lets.h
index 75ca347..accc056 100644
--- a/src/transform/inline_pointer_lets.h
+++ b/src/transform/inline_pointer_lets.h
@@ -31,7 +31,7 @@
 /// Note: InlinePointerLets does not operate on module-scope `let`s, as these
 /// cannot be pointers: https://gpuweb.github.io/gpuweb/wgsl/#module-constants
 /// `A module-scope let-declared constant must be of atomic-free plain type.`
-class InlinePointerLets : public Transform {
+class InlinePointerLets : public Castable<InlinePointerLets, Transform> {
  public:
   /// Constructor
   InlinePointerLets();
@@ -39,11 +39,14 @@
   /// Destructor
   ~InlinePointerLets() 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/manager.cc b/src/transform/manager.cc
index 10e3f58..0c1a0f0 100644
--- a/src/transform/manager.cc
+++ b/src/transform/manager.cc
@@ -14,6 +14,8 @@
 
 #include "src/transform/manager.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::Manager);
+
 namespace tint {
 namespace transform {
 
diff --git a/src/transform/manager.h b/src/transform/manager.h
index 345afb7..8d31bb5 100644
--- a/src/transform/manager.h
+++ b/src/transform/manager.h
@@ -28,7 +28,7 @@
 /// The inner transforms will execute in the appended order.
 /// If any inner transform fails the manager will return immediately and
 /// the error can be retrieved with the Output's diagnostics.
-class Manager : public Transform {
+class Manager : public Castable<Manager, Transform> {
  public:
   /// Constructor
   Manager();
diff --git a/src/transform/msl.cc b/src/transform/msl.cc
index c89a29d..b1c4605 100644
--- a/src/transform/msl.cc
+++ b/src/transform/msl.cc
@@ -36,6 +36,7 @@
 #include "src/transform/wrap_arrays_in_structs.h"
 #include "src/transform/zero_init_workgroup_memory.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::Msl);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::Msl::Config);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::Msl::Result);
 
@@ -103,6 +104,8 @@
 
   auto result = std::make_unique<Result>(
       out.data.Get<ArrayLengthFromUniform::Result>()->needs_buffer_sizes);
+
+  builder.SetTransformApplied(this);
   return Output{Program(std::move(builder)), std::move(result)};
 }
 
diff --git a/src/transform/msl.h b/src/transform/msl.h
index 001dfe0..0fb6cb5 100644
--- a/src/transform/msl.h
+++ b/src/transform/msl.h
@@ -23,7 +23,7 @@
 /// Msl is a transform used to sanitize a Program for use with the Msl writer.
 /// Passing a non-sanitized Program to the Msl writer will result in undefined
 /// behavior.
-class Msl : public Transform {
+class Msl : public Castable<Msl, Transform> {
  public:
   /// The default buffer slot to use for the storage buffer size buffer.
   const uint32_t kDefaultBufferSizeUniformIndex = 30;
diff --git a/src/transform/pad_array_elements.cc b/src/transform/pad_array_elements.cc
index 24268f0..a6e3351 100644
--- a/src/transform/pad_array_elements.cc
+++ b/src/transform/pad_array_elements.cc
@@ -22,6 +22,8 @@
 #include "src/sem/expression.h"
 #include "src/utils/get_or_create.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::PadArrayElements);
+
 namespace tint {
 namespace transform {
 namespace {
@@ -89,10 +91,7 @@
 
 PadArrayElements::~PadArrayElements() = default;
 
-Output PadArrayElements::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
+void PadArrayElements::Run(CloneContext& ctx, const DataMap&, DataMap&) {
   auto& sem = ctx.src->Sem();
 
   std::unordered_map<const sem::Array*, ArrayBuilder> padded_arrays;
@@ -149,8 +148,6 @@
   });
 
   ctx.Clone();
-
-  return Output(Program(std::move(out)));
 }
 
 }  // namespace transform
diff --git a/src/transform/pad_array_elements.h b/src/transform/pad_array_elements.h
index db9f215..cbb3e14 100644
--- a/src/transform/pad_array_elements.h
+++ b/src/transform/pad_array_elements.h
@@ -30,7 +30,7 @@
 /// structure element type.
 /// This transform helps with backends that cannot directly return arrays or use
 /// them as parameters.
-class PadArrayElements : public Transform {
+class PadArrayElements : public Castable<PadArrayElements, Transform> {
  public:
   /// Constructor
   PadArrayElements();
@@ -38,11 +38,14 @@
   /// Destructor
   ~PadArrayElements() 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/promote_initializers_to_const_var.cc b/src/transform/promote_initializers_to_const_var.cc
index d0724d3..87e7976 100644
--- a/src/transform/promote_initializers_to_const_var.cc
+++ b/src/transform/promote_initializers_to_const_var.cc
@@ -21,6 +21,8 @@
 #include "src/sem/expression.h"
 #include "src/sem/statement.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::PromoteInitializersToConstVar);
+
 namespace tint {
 namespace transform {
 
@@ -28,10 +30,9 @@
 
 PromoteInitializersToConstVar::~PromoteInitializersToConstVar() = default;
 
-Output PromoteInitializersToConstVar::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
+void PromoteInitializersToConstVar::Run(CloneContext& ctx,
+                                        const DataMap&,
+                                        DataMap&) {
   // Scan the AST nodes for array and structure initializers which
   // need to be promoted to their own constant declaration.
 
@@ -100,8 +101,6 @@
   }
 
   ctx.Clone();
-
-  return Output(Program(std::move(out)));
 }
 
 }  // namespace transform
diff --git a/src/transform/promote_initializers_to_const_var.h b/src/transform/promote_initializers_to_const_var.h
index 6162363..59adfb7 100644
--- a/src/transform/promote_initializers_to_const_var.h
+++ b/src/transform/promote_initializers_to_const_var.h
@@ -23,7 +23,8 @@
 /// A transform that hoists the array and structure initializers to a constant
 /// variable, declared just before the statement of usage. See
 /// crbug.com/tint/406 for more details.
-class PromoteInitializersToConstVar : public Transform {
+class PromoteInitializersToConstVar
+    : public Castable<PromoteInitializersToConstVar, Transform> {
  public:
   /// Constructor
   PromoteInitializersToConstVar();
@@ -31,11 +32,14 @@
   /// Destructor
   ~PromoteInitializersToConstVar() 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/renamer.cc b/src/transform/renamer.cc
index c39171f..b6f6b78 100644
--- a/src/transform/renamer.cc
+++ b/src/transform/renamer.cc
@@ -22,7 +22,9 @@
 #include "src/sem/call.h"
 #include "src/sem/member_accessor_expression.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::Renamer);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::Renamer::Data);
+TINT_INSTANTIATE_TYPEINFO(tint::transform::Renamer::Config);
 
 namespace tint {
 namespace transform {
@@ -835,18 +837,18 @@
 }  // namespace
 
 Renamer::Data::Data(Remappings&& r) : remappings(std::move(r)) {}
-
 Renamer::Data::Data(const Data&) = default;
-
 Renamer::Data::~Data() = default;
 
-Renamer::Renamer() : cfg_{} {}
+Renamer::Config::Config(Target t) : target(t) {}
+Renamer::Config::Config(const Config&) = default;
+Renamer::Config::~Config() = default;
 
-Renamer::Renamer(const Config& config) : cfg_(config) {}
-
+Renamer::Renamer() : deprecated_cfg_(Target::kAll) {}
+Renamer::Renamer(const Config& config) : deprecated_cfg_(config) {}
 Renamer::~Renamer() = default;
 
-Output Renamer::Run(const Program* in, const DataMap&) {
+Output Renamer::Run(const Program* in, const DataMap& inputs) {
   ProgramBuilder out;
   // Disable auto-cloning of symbols, since we want to rename them.
   CloneContext ctx(&out, in, false);
@@ -879,9 +881,14 @@
 
   Data::Remappings remappings;
 
+  auto* cfg = inputs.Get<Config>();
+  if (!cfg) {
+    cfg = &deprecated_cfg_;
+  }
+
   ctx.ReplaceAll([&](Symbol sym_in) {
     auto name_in = ctx.src->Symbols().NameFor(sym_in);
-    switch (cfg_.target) {
+    switch (cfg->target) {
       case Target::kAll:
         // Always rename.
         break;
diff --git a/src/transform/renamer.h b/src/transform/renamer.h
index 55cf5dc..33e9142 100644
--- a/src/transform/renamer.h
+++ b/src/transform/renamer.h
@@ -24,7 +24,7 @@
 namespace transform {
 
 /// Renamer is a Transform that renames all the symbols in a program.
-class Renamer : public Transform {
+class Renamer : public Castable<Renamer, Transform> {
  public:
   /// Data is outputted by the Renamer transform.
   /// Data holds information about shader usage and constant buffer offsets.
@@ -57,16 +57,27 @@
   };
 
   /// Configuration options for the transform
-  struct Config {
+  struct Config : public Castable<Config, transform::Data> {
+    /// Constructor
+    /// @param tgt the targets to rename
+    explicit Config(Target tgt);
+
+    /// Copy constructor
+    Config(const Config&);
+
+    /// Destructor
+    ~Config() override;
+
     /// The targets to rename
-    Target target = Target::kAll;
+    Target const target = Target::kAll;
   };
 
-  /// Constructor using a default configuration
+  /// Constructor using a the configuration provided in the input Data
   Renamer();
 
   /// Constructor
   /// @param config the configuration for the transform
+  /// [DEPRECATED] Pass Config as input Data
   explicit Renamer(const Config& config);
 
   /// Destructor
@@ -79,7 +90,7 @@
   Output Run(const Program* program, const DataMap& data = {}) override;
 
  private:
-  Config const cfg_;
+  Config const deprecated_cfg_;
 };
 
 }  // namespace transform
diff --git a/src/transform/renamer_test.cc b/src/transform/renamer_test.cc
index ca2bc44..73467a0 100644
--- a/src/transform/renamer_test.cc
+++ b/src/transform/renamer_test.cc
@@ -207,8 +207,9 @@
 }
 )";
 
-  Renamer::Config config{Renamer::Target::kHlslKeywords};
-  auto got = Run(src, std::make_unique<Renamer>(config));
+  DataMap inputs;
+  inputs.Add<Renamer::Config>(Renamer::Target::kHlslKeywords);
+  auto got = Run<Renamer>(src, inputs);
 
   EXPECT_EQ(expect, str(got));
 }
@@ -231,8 +232,9 @@
 }
 )";
 
-  Renamer::Config config{Renamer::Target::kMslKeywords};
-  auto got = Run(src, std::make_unique<Renamer>(config));
+  DataMap inputs;
+  inputs.Add<Renamer::Config>(Renamer::Target::kMslKeywords);
+  auto got = Run<Renamer>(src, inputs);
 
   EXPECT_EQ(expect, str(got));
 }
diff --git a/src/transform/simplify.cc b/src/transform/simplify.cc
index c9ac2ef..c007d35 100644
--- a/src/transform/simplify.cc
+++ b/src/transform/simplify.cc
@@ -25,6 +25,8 @@
 #include "src/sem/variable.h"
 #include "src/utils/scoped_assignment.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::Simplify);
+
 namespace tint {
 namespace transform {
 
@@ -32,10 +34,7 @@
 
 Simplify::~Simplify() = default;
 
-Output Simplify::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
+void Simplify::Run(CloneContext& ctx, const DataMap&, DataMap&) {
   ctx.ReplaceAll([&](ast::Expression* expr) -> ast::Expression* {
     if (auto* outer = expr->As<ast::UnaryOpExpression>()) {
       if (auto* inner = outer->expr()->As<ast::UnaryOpExpression>()) {
@@ -55,8 +54,6 @@
   });
 
   ctx.Clone();
-
-  return Output(Program(std::move(out)));
 }
 
 }  // namespace transform
diff --git a/src/transform/simplify.h b/src/transform/simplify.h
index f6fe5b5..084e0ba 100644
--- a/src/transform/simplify.h
+++ b/src/transform/simplify.h
@@ -28,7 +28,7 @@
 /// Simplify currently optimizes the following:
 /// `&(*(expr))` => `expr`
 /// `*(&(expr))` => `expr`
-class Simplify : public Transform {
+class Simplify : public Castable<Simplify, Transform> {
  public:
   /// Constructor
   Simplify();
@@ -36,11 +36,14 @@
   /// Destructor
   ~Simplify() 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/single_entry_point.cc b/src/transform/single_entry_point.cc
index 15afa5f..c8ece46 100644
--- a/src/transform/single_entry_point.cc
+++ b/src/transform/single_entry_point.cc
@@ -21,6 +21,7 @@
 #include "src/sem/function.h"
 #include "src/sem/variable.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::SingleEntryPoint);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::SingleEntryPoint::Config);
 
 namespace tint {
@@ -30,69 +31,63 @@
 
 SingleEntryPoint::~SingleEntryPoint() = default;
 
-Output SingleEntryPoint::Run(const Program* in, const DataMap& data) {
-  ProgramBuilder out;
-
-  auto* cfg = data.Get<Config>();
+void SingleEntryPoint::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) {
+  auto* cfg = inputs.Get<Config>();
   if (cfg == nullptr) {
-    out.Diagnostics().add_error(diag::System::Transform,
-                                "missing transform data for SingleEntryPoint");
-    return Output(Program(std::move(out)));
+    ctx.dst->Diagnostics().add_error(
+        diag::System::Transform, "missing transform data for SingleEntryPoint");
+    return;
   }
 
   // Find the target entry point.
   ast::Function* entry_point = nullptr;
-  for (auto* f : in->AST().Functions()) {
+  for (auto* f : ctx.src->AST().Functions()) {
     if (!f->IsEntryPoint()) {
       continue;
     }
-    if (in->Symbols().NameFor(f->symbol()) == cfg->entry_point_name) {
+    if (ctx.src->Symbols().NameFor(f->symbol()) == cfg->entry_point_name) {
       entry_point = f;
       break;
     }
   }
   if (entry_point == nullptr) {
-    out.Diagnostics().add_error(
+    ctx.dst->Diagnostics().add_error(
         diag::System::Transform,
         "entry point '" + cfg->entry_point_name + "' not found");
-    return Output(Program(std::move(out)));
+    return;
   }
 
-  CloneContext ctx(&out, in);
-
-  auto* sem = in->Sem().Get(entry_point);
+  auto& sem = ctx.src->Sem();
 
   // Build set of referenced module-scope variables for faster lookups later.
   std::unordered_set<const ast::Variable*> referenced_vars;
-  for (auto* var : sem->ReferencedModuleVariables()) {
+  for (auto* var : sem.Get(entry_point)->ReferencedModuleVariables()) {
     referenced_vars.emplace(var->Declaration());
   }
 
   // Clone any module-scope variables, types, and functions that are statically
   // referenced by the target entry point.
-  for (auto* decl : in->AST().GlobalDeclarations()) {
+  for (auto* decl : ctx.src->AST().GlobalDeclarations()) {
     if (auto* ty = decl->As<ast::TypeDecl>()) {
       // TODO(jrprice): Strip unused types.
-      out.AST().AddTypeDecl(ctx.Clone(ty));
+      ctx.dst->AST().AddTypeDecl(ctx.Clone(ty));
     } else if (auto* var = decl->As<ast::Variable>()) {
       if (var->is_const() || referenced_vars.count(var)) {
-        out.AST().AddGlobalVariable(ctx.Clone(var));
+        ctx.dst->AST().AddGlobalVariable(ctx.Clone(var));
       }
     } else if (auto* func = decl->As<ast::Function>()) {
-      if (in->Sem().Get(func)->HasAncestorEntryPoint(entry_point->symbol())) {
-        out.AST().AddFunction(ctx.Clone(func));
+      if (sem.Get(func)->HasAncestorEntryPoint(entry_point->symbol())) {
+        ctx.dst->AST().AddFunction(ctx.Clone(func));
       }
     } else {
-      TINT_UNREACHABLE(Transform, out.Diagnostics())
+      TINT_UNREACHABLE(Transform, ctx.dst->Diagnostics())
           << "unhandled global declaration: " << decl->TypeInfo().name;
-      return Output(Program(std::move(out)));
+      return;
     }
   }
 
   // Clone the entry point.
-  out.AST().AddFunction(ctx.Clone(entry_point));
-
-  return Output(Program(std::move(out)));
+  ctx.dst->AST().AddFunction(ctx.Clone(entry_point));
 }
 
 SingleEntryPoint::Config::Config(std::string entry_point)
diff --git a/src/transform/single_entry_point.h b/src/transform/single_entry_point.h
index c2cd16c..447b5c4 100644
--- a/src/transform/single_entry_point.h
+++ b/src/transform/single_entry_point.h
@@ -26,7 +26,7 @@
 ///
 /// All module-scope variables, types, and functions that are not used by the
 /// target entry point will also be removed.
-class SingleEntryPoint : public Transform {
+class SingleEntryPoint : public Castable<SingleEntryPoint, Transform> {
  public:
   /// Configuration options for the transform
   struct Config : public Castable<Config, Data> {
@@ -54,11 +54,14 @@
   /// Destructor
   ~SingleEntryPoint() 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 = {}) 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) override;
 };
 
 }  // namespace transform
diff --git a/src/transform/spirv.cc b/src/transform/spirv.cc
index 874c114..b88a427 100644
--- a/src/transform/spirv.cc
+++ b/src/transform/spirv.cc
@@ -34,6 +34,7 @@
 #include "src/transform/simplify.h"
 #include "src/transform/zero_init_workgroup_memory.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::Spirv);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::Spirv::Config);
 
 namespace tint {
@@ -70,6 +71,7 @@
   }
   ctx2.Clone();
 
+  out2.SetTransformApplied(this);
   return Output{Program(std::move(out2))};
 }
 
diff --git a/src/transform/spirv.h b/src/transform/spirv.h
index febf5bb..dba32b5 100644
--- a/src/transform/spirv.h
+++ b/src/transform/spirv.h
@@ -29,7 +29,7 @@
 /// Spirv is a transform used to sanitize a Program for use with the Spirv
 /// writer. Passing a non-sanitized Program to the Spirv writer will result in
 /// undefined behavior.
-class Spirv : public Transform {
+class Spirv : public Castable<Spirv, Transform> {
  public:
   /// Configuration options for the transform.
   struct Config : public Castable<Config, Data> {
diff --git a/src/transform/test_helper.h b/src/transform/test_helper.h
index dcd11b0..ed21a60 100644
--- a/src/transform/test_helper.h
+++ b/src/transform/test_helper.h
@@ -33,32 +33,6 @@
 class TransformTestBase : public BASE {
  public:
   /// Transforms and returns the WGSL source `in`, transformed using
-  /// `transforms`.
-  /// @param in the input WGSL source
-  /// @param transforms the list of transforms to apply
-  /// @param data the optional DataMap to pass to Transform::Run()
-  /// @return the transformed output
-  Output Run(std::string in,
-             std::vector<std::unique_ptr<transform::Transform>> transforms,
-             const DataMap& data = {}) {
-    auto file = std::make_unique<Source::File>("test", in);
-    auto program = reader::wgsl::Parse(file.get());
-
-    // Keep this pointer alive after Transform() returns
-    files_.emplace_back(std::move(file));
-
-    if (!program.IsValid()) {
-      return Output(std::move(program));
-    }
-
-    Manager manager;
-    for (auto& transform : transforms) {
-      manager.append(std::move(transform));
-    }
-    return manager.Run(&program, data);
-  }
-
-  /// Transforms and returns the WGSL source `in`, transformed using
   /// `transform`.
   /// @param transform the transform to apply
   /// @param in the input WGSL source
@@ -77,9 +51,24 @@
   /// @param in the input WGSL source
   /// @param data the optional DataMap to pass to Transform::Run()
   /// @return the transformed output
-  template <typename TRANSFORM>
+  template <typename... TRANSFORMS>
   Output Run(std::string in, const DataMap& data = {}) {
-    return Run(std::move(in), std::make_unique<TRANSFORM>(), data);
+    auto file = std::make_unique<Source::File>("test", in);
+    auto program = reader::wgsl::Parse(file.get());
+
+    // Keep this pointer alive after Transform() returns
+    files_.emplace_back(std::move(file));
+
+    if (!program.IsValid()) {
+      return Output(std::move(program));
+    }
+
+    Manager manager;
+    for (auto* transform_ptr :
+         std::initializer_list<Transform*>{new TRANSFORMS()...}) {
+      manager.append(std::unique_ptr<Transform>(transform_ptr));
+    }
+    return manager.Run(&program, data);
   }
 
   /// @param output the output of the transform
diff --git a/src/transform/transform.cc b/src/transform/transform.cc
index 914b167..a6b46bd 100644
--- a/src/transform/transform.cc
+++ b/src/transform/transform.cc
@@ -15,11 +15,13 @@
 #include "src/transform/transform.h"
 
 #include <algorithm>
+#include <string>
 
 #include "src/program_builder.h"
 #include "src/sem/atomic_type.h"
 #include "src/sem/reference_type.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::Transform);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::Data);
 
 namespace tint {
@@ -40,6 +42,35 @@
 Transform::Transform() = default;
 Transform::~Transform() = default;
 
+Output Transform::Run(const Program* program, const DataMap& data /* = {} */) {
+  ProgramBuilder builder;
+  CloneContext ctx(&builder, program);
+  Output output;
+  Run(ctx, data, output.data);
+  builder.SetTransformApplied(this);
+  output.program = Program(std::move(builder));
+  return output;
+}
+
+void Transform::Run(CloneContext& ctx, const DataMap&, DataMap&) {
+  TINT_UNIMPLEMENTED(Transform, ctx.dst->Diagnostics())
+      << "Transform::Run() unimplemented for " << TypeInfo().name;
+}
+
+bool Transform::Requires(CloneContext& ctx,
+                         std::initializer_list<const ::tint::TypeInfo*> deps) {
+  for (auto* dep : deps) {
+    if (!ctx.src->HasTransformApplied(dep)) {
+      ctx.dst->Diagnostics().add_error(
+          diag::System::Transform, std::string(TypeInfo().name) +
+                                       " depends on " + std::string(dep->name) +
+                                       " but the dependency was not run");
+      return false;
+    }
+  }
+  return true;
+}
+
 ast::Function* Transform::CloneWithStatementsAtStart(
     CloneContext* ctx,
     ast::Function* in,
diff --git a/src/transform/transform.h b/src/transform/transform.h
index 3506af1..b589ab5 100644
--- a/src/transform/transform.h
+++ b/src/transform/transform.h
@@ -19,6 +19,7 @@
 #include <unordered_map>
 #include <utility>
 
+#include "src/castable.h"
 #include "src/program.h"
 
 namespace tint {
@@ -145,20 +146,45 @@
 };
 
 /// Interface for Program transforms
-class Transform {
+class Transform : public Castable<Transform> {
  public:
   /// Constructor
   Transform();
   /// Destructor
-  virtual ~Transform();
+  ~Transform() 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
-  virtual Output Run(const Program* program, const DataMap& data = {}) = 0;
+  virtual Output Run(const Program* program, const DataMap& data = {});
 
  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
+  virtual void Run(CloneContext& ctx, const DataMap& inputs, DataMap& outputs);
+
+  /// Requires appends an error diagnostic to `ctx.dst` if the template type
+  /// transforms were not already run on `ctx.src`.
+  /// @param ctx the CloneContext
+  /// @returns true if all dependency transforms have been run
+  template <typename... TRANSFORMS>
+  bool Requires(CloneContext& ctx) {
+    return Requires(ctx, {&::tint::TypeInfo::Of<TRANSFORMS>()...});
+  }
+
+  /// Requires appends an error diagnostic to `ctx.dst` if the list of
+  /// Transforms were not already run on `ctx.src`.
+  /// @param ctx the CloneContext
+  /// @param deps the list of Transform TypeInfos
+  /// @returns true if all dependency transforms have been run
+  bool Requires(CloneContext& ctx,
+                std::initializer_list<const ::tint::TypeInfo*> deps);
+
   /// Clones the function `in` adding `statements` to the beginning of the
   /// cloned function body.
   /// @param ctx the clone context
diff --git a/src/transform/vertex_pulling.cc b/src/transform/vertex_pulling.cc
index e06dd7c..1161de9 100644
--- a/src/transform/vertex_pulling.cc
+++ b/src/transform/vertex_pulling.cc
@@ -24,6 +24,7 @@
 #include "src/sem/variable.h"
 #include "src/utils/get_or_create.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::VertexPulling);
 TINT_INSTANTIATE_TYPEINFO(tint::transform::VertexPulling::Config);
 
 namespace tint {
@@ -456,21 +457,20 @@
 VertexPulling::VertexPulling() = default;
 VertexPulling::~VertexPulling() = default;
 
-Output VertexPulling::Run(const Program* in, const DataMap& data) {
-  ProgramBuilder out;
-
+void VertexPulling::Run(CloneContext& ctx, const DataMap& inputs, DataMap&) {
   auto cfg = cfg_;
-  if (auto* cfg_data = data.Get<Config>()) {
+  if (auto* cfg_data = inputs.Get<Config>()) {
     cfg = *cfg_data;
   }
 
   // Find entry point
-  auto* func = in->AST().Functions().Find(
-      in->Symbols().Get(cfg.entry_point_name), ast::PipelineStage::kVertex);
+  auto* func = ctx.src->AST().Functions().Find(
+      ctx.src->Symbols().Get(cfg.entry_point_name),
+      ast::PipelineStage::kVertex);
   if (func == nullptr) {
-    out.Diagnostics().add_error(diag::System::Transform,
-                                "Vertex stage entry point not found");
-    return Output(Program(std::move(out)));
+    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
@@ -479,15 +479,11 @@
   // TODO(idanr): Make sure we covered all error cases, to guarantee the
   // following stages will pass
 
-  CloneContext ctx(&out, in);
-
   State state{ctx, cfg};
   state.AddVertexStorageBuffers();
   state.Process(func);
 
   ctx.Clone();
-
-  return Output(Program(std::move(out)));
 }
 
 VertexPulling::Config::Config() = default;
diff --git a/src/transform/vertex_pulling.h b/src/transform/vertex_pulling.h
index 15ea211..6affca4 100644
--- a/src/transform/vertex_pulling.h
+++ b/src/transform/vertex_pulling.h
@@ -130,7 +130,7 @@
 /// code, but these are types that the data may arrive as. We need to convert
 /// these smaller types into the base types such as `f32` and `u32` for the
 /// shader to use.
-class VertexPulling : public Transform {
+class VertexPulling : public Castable<VertexPulling, Transform> {
  public:
   /// Configuration options for the transform
   struct Config : public Castable<Config, Data> {
@@ -164,11 +164,14 @@
   /// Destructor
   ~VertexPulling() 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 = {}) 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) override;
 
  private:
   Config cfg_;
diff --git a/src/transform/wrap_arrays_in_structs.cc b/src/transform/wrap_arrays_in_structs.cc
index b1715aa..d7c7396 100644
--- a/src/transform/wrap_arrays_in_structs.cc
+++ b/src/transform/wrap_arrays_in_structs.cc
@@ -21,6 +21,8 @@
 #include "src/sem/expression.h"
 #include "src/utils/get_or_create.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::WrapArraysInStructs);
+
 namespace tint {
 namespace transform {
 
@@ -33,10 +35,7 @@
 
 WrapArraysInStructs::~WrapArraysInStructs() = default;
 
-Output WrapArraysInStructs::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
+void WrapArraysInStructs::Run(CloneContext& ctx, const DataMap&, DataMap&) {
   auto& sem = ctx.src->Sem();
 
   std::unordered_map<const sem::Array*, WrappedArrayInfo> wrapped_arrays;
@@ -60,8 +59,8 @@
   // Fix up array accessors so `a[1]` becomes `a.arr[1]`
   ctx.ReplaceAll([&](ast::ArrayAccessorExpression* accessor)
                      -> ast::ArrayAccessorExpression* {
-    if (auto* array =
-            As<sem::Array>(sem.Get(accessor->array())->Type()->UnwrapRef())) {
+    if (auto* array = ::tint::As<sem::Array>(
+            sem.Get(accessor->array())->Type()->UnwrapRef())) {
       if (wrapper(array)) {
         // Array is wrapped in a structure. Emit a member accessor to get
         // to the actual array.
@@ -76,7 +75,8 @@
 
   // Fix up array constructors so `A(1,2)` becomes `tint_array_wrapper(A(1,2))`
   ctx.ReplaceAll([&](ast::TypeConstructorExpression* ctor) -> ast::Expression* {
-    if (auto* array = As<sem::Array>(sem.Get(ctor)->Type()->UnwrapRef())) {
+    if (auto* array =
+            ::tint::As<sem::Array>(sem.Get(ctor)->Type()->UnwrapRef())) {
       if (auto w = wrapper(array)) {
         // Wrap the array type constructor with another constructor for
         // the wrapper
@@ -91,8 +91,6 @@
   });
 
   ctx.Clone();
-
-  return Output(Program(std::move(out)));
 }
 
 WrapArraysInStructs::WrappedArrayInfo WrapArraysInStructs::WrapArray(
diff --git a/src/transform/wrap_arrays_in_structs.h b/src/transform/wrap_arrays_in_structs.h
index 2dda1ee..6eb4bc1 100644
--- a/src/transform/wrap_arrays_in_structs.h
+++ b/src/transform/wrap_arrays_in_structs.h
@@ -36,7 +36,7 @@
 /// wrapping.
 /// This transform helps with backends that cannot directly return arrays or use
 /// them as parameters.
-class WrapArraysInStructs : public Transform {
+class WrapArraysInStructs : public Castable<WrapArraysInStructs, Transform> {
  public:
   /// Constructor
   WrapArraysInStructs();
@@ -44,11 +44,14 @@
   /// Destructor
   ~WrapArraysInStructs() 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 = {}) 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) override;
 
  private:
   struct WrappedArrayInfo {
diff --git a/src/transform/zero_init_workgroup_memory.cc b/src/transform/zero_init_workgroup_memory.cc
index 287018c..80ba53a 100644
--- a/src/transform/zero_init_workgroup_memory.cc
+++ b/src/transform/zero_init_workgroup_memory.cc
@@ -23,6 +23,8 @@
 #include "src/sem/variable.h"
 #include "src/utils/get_or_create.h"
 
+TINT_INSTANTIATE_TYPEINFO(tint::transform::ZeroInitWorkgroupMemory);
+
 namespace tint {
 namespace transform {
 
@@ -111,13 +113,10 @@
 
 ZeroInitWorkgroupMemory::~ZeroInitWorkgroupMemory() = default;
 
-Output ZeroInitWorkgroupMemory::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
-
+void ZeroInitWorkgroupMemory::Run(CloneContext& ctx, const DataMap&, DataMap&) {
   auto& sem = ctx.src->Sem();
 
-  for (auto* ast_func : in->AST().Functions()) {
+  for (auto* ast_func : ctx.src->AST().Functions()) {
     if (!ast_func->IsEntryPoint()) {
       continue;
     }
@@ -192,8 +191,6 @@
   }
 
   ctx.Clone();
-
-  return Output(Program(std::move(out)));
 }
 
 }  // namespace transform
diff --git a/src/transform/zero_init_workgroup_memory.h b/src/transform/zero_init_workgroup_memory.h
index bf846c7..1644b4d 100644
--- a/src/transform/zero_init_workgroup_memory.h
+++ b/src/transform/zero_init_workgroup_memory.h
@@ -23,7 +23,8 @@
 /// ZeroInitWorkgroupMemory is a transform that injects code at the top of entry
 /// points to zero-initialize workgroup memory used by that entry point (and all
 /// transitive functions called by that entry point)
-class ZeroInitWorkgroupMemory : public Transform {
+class ZeroInitWorkgroupMemory
+    : public Castable<ZeroInitWorkgroupMemory, Transform> {
  public:
   /// Constructor
   ZeroInitWorkgroupMemory();
@@ -31,11 +32,14 @@
   /// Destructor
   ~ZeroInitWorkgroupMemory() 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 = {}) 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) override;
 
  private:
   struct State;
diff --git a/src/writer/hlsl/generator_impl.cc b/src/writer/hlsl/generator_impl.cc
index ce1aea8..f7677e4 100644
--- a/src/writer/hlsl/generator_impl.cc
+++ b/src/writer/hlsl/generator_impl.cc
@@ -36,6 +36,7 @@
 #include "src/sem/struct.h"
 #include "src/sem/variable.h"
 #include "src/transform/calculate_array_length.h"
+#include "src/transform/hlsl.h"
 #include "src/utils/scoped_assignment.h"
 #include "src/writer/append_vector.h"
 #include "src/writer/float_to_string.h"
@@ -114,6 +115,14 @@
 GeneratorImpl::~GeneratorImpl() = default;
 
 bool GeneratorImpl::Generate(std::ostream& out) {
+  if (!builder_.HasTransformApplied<transform::Hlsl>()) {
+    diagnostics_.add_error(
+        diag::System::Writer,
+        "HLSL writer requires the transform::Hlsl sanitizer to have been "
+        "applied to the input program");
+    return false;
+  }
+
   std::stringstream pending;
   const TypeInfo* last_kind = nullptr;
 
diff --git a/src/writer/hlsl/generator_impl_test.cc b/src/writer/hlsl/generator_impl_test.cc
index 341b2d1..adf73e4 100644
--- a/src/writer/hlsl/generator_impl_test.cc
+++ b/src/writer/hlsl/generator_impl_test.cc
@@ -21,6 +21,16 @@
 
 using HlslGeneratorImplTest = TestHelper;
 
+TEST_F(HlslGeneratorImplTest, ErrorIfSanitizerNotRun) {
+  auto program = std::make_unique<Program>(std::move(*this));
+  GeneratorImpl gen(program.get());
+  EXPECT_FALSE(gen.Generate(out));
+  EXPECT_EQ(
+      gen.error(),
+      "error: HLSL writer requires the transform::Hlsl sanitizer to have been "
+      "applied to the input program");
+}
+
 TEST_F(HlslGeneratorImplTest, Generate) {
   Func("my_func", ast::VariableList{}, ty.void_(), ast::StatementList{},
        ast::DecorationList{});
diff --git a/src/writer/hlsl/test_helper.h b/src/writer/hlsl/test_helper.h
index 6ccbb3b..26c5563 100644
--- a/src/writer/hlsl/test_helper.h
+++ b/src/writer/hlsl/test_helper.h
@@ -44,15 +44,17 @@
     if (gen_) {
       return *gen_;
     }
-    diag::Formatter formatter;
+    // Fake that the HLSL sanitizer has been applied, so that we can unit test
+    // the writer without it erroring.
+    SetTransformApplied<transform::Hlsl>();
     [&]() {
       ASSERT_TRUE(IsValid()) << "Builder program is not valid\n"
-                             << formatter.format(Diagnostics());
+                             << diag::Formatter().format(Diagnostics());
     }();
     program = std::make_unique<Program>(std::move(*this));
     [&]() {
       ASSERT_TRUE(program->IsValid())
-          << formatter.format(program->Diagnostics());
+          << diag::Formatter().format(program->Diagnostics());
     }();
     gen_ = std::make_unique<GeneratorImpl>(program.get());
     return *gen_;
diff --git a/src/writer/msl/generator_impl.cc b/src/writer/msl/generator_impl.cc
index 5a89d11..db3665e 100644
--- a/src/writer/msl/generator_impl.cc
+++ b/src/writer/msl/generator_impl.cc
@@ -50,6 +50,7 @@
 #include "src/sem/variable.h"
 #include "src/sem/vector_type.h"
 #include "src/sem/void_type.h"
+#include "src/transform/msl.h"
 #include "src/utils/scoped_assignment.h"
 #include "src/writer/float_to_string.h"
 
@@ -75,6 +76,14 @@
 GeneratorImpl::~GeneratorImpl() = default;
 
 bool GeneratorImpl::Generate() {
+  if (!program_->HasTransformApplied<transform::Msl>()) {
+    diagnostics_.add_error(
+        diag::System::Writer,
+        "MSL writer requires the transform::Msl sanitizer to have been "
+        "applied to the input program");
+    return false;
+  }
+
   out_ << "#include <metal_stdlib>" << std::endl << std::endl;
   out_ << "using namespace metal;" << std::endl;
 
diff --git a/src/writer/msl/generator_impl_test.cc b/src/writer/msl/generator_impl_test.cc
index 4cb99f8..46bdef5 100644
--- a/src/writer/msl/generator_impl_test.cc
+++ b/src/writer/msl/generator_impl_test.cc
@@ -22,6 +22,16 @@
 
 using MslGeneratorImplTest = TestHelper;
 
+TEST_F(MslGeneratorImplTest, ErrorIfSanitizerNotRun) {
+  auto program = std::make_unique<Program>(std::move(*this));
+  GeneratorImpl gen(program.get());
+  EXPECT_FALSE(gen.Generate());
+  EXPECT_EQ(
+      gen.error(),
+      "error: MSL writer requires the transform::Msl sanitizer to have been "
+      "applied to the input program");
+}
+
 TEST_F(MslGeneratorImplTest, Generate) {
   Func("my_func", ast::VariableList{}, ty.void_(), ast::StatementList{},
        ast::DecorationList{
diff --git a/src/writer/msl/test_helper.h b/src/writer/msl/test_helper.h
index 3ae78c7..7400467 100644
--- a/src/writer/msl/test_helper.h
+++ b/src/writer/msl/test_helper.h
@@ -43,6 +43,9 @@
     if (gen_) {
       return *gen_;
     }
+    // Fake that the MSL sanitizer has been applied, so that we can unit test
+    // the writer without it erroring.
+    SetTransformApplied<transform::Msl>();
     [&]() {
       ASSERT_TRUE(IsValid()) << "Builder program is not valid\n"
                              << diag::Formatter().format(Diagnostics());
diff --git a/src/writer/spirv/builder.cc b/src/writer/spirv/builder.cc
index e6bc0a8..4af004a 100644
--- a/src/writer/spirv/builder.cc
+++ b/src/writer/spirv/builder.cc
@@ -35,6 +35,7 @@
 #include "src/sem/struct.h"
 #include "src/sem/variable.h"
 #include "src/sem/vector_type.h"
+#include "src/transform/spirv.h"
 #include "src/utils/get_or_create.h"
 #include "src/writer/append_vector.h"
 
@@ -258,6 +259,13 @@
 Builder::~Builder() = default;
 
 bool Builder::Build() {
+  if (!builder_.HasTransformApplied<transform::Spirv>()) {
+    error_ =
+        "SPIR-V writer requires the transform::Spirv sanitizer to have been "
+        "applied to the input program";
+    return false;
+  }
+
   push_capability(SpvCapabilityShader);
 
   push_memory_model(spv::Op::OpMemoryModel,
diff --git a/src/writer/spirv/builder_test.cc b/src/writer/spirv/builder_test.cc
index 20f23b4..acf48d6 100644
--- a/src/writer/spirv/builder_test.cc
+++ b/src/writer/spirv/builder_test.cc
@@ -22,6 +22,16 @@
 
 using BuilderTest = TestHelper;
 
+TEST_F(BuilderTest, ErrorIfSanitizerNotRun) {
+  auto program = std::make_unique<Program>(std::move(*this));
+  spirv::Builder b(program.get());
+  EXPECT_FALSE(b.Build());
+  EXPECT_EQ(
+      b.error(),
+      "SPIR-V writer requires the transform::Spirv sanitizer to have been "
+      "applied to the input program");
+}
+
 TEST_F(BuilderTest, InsertsPreamble) {
   spirv::Builder& b = Build();
 
diff --git a/src/writer/spirv/test_helper.h b/src/writer/spirv/test_helper.h
index 0fe99e7..dd8f5c2 100644
--- a/src/writer/spirv/test_helper.h
+++ b/src/writer/spirv/test_helper.h
@@ -43,6 +43,9 @@
     if (spirv_builder) {
       return *spirv_builder;
     }
+    // Fake that the SPIR-V sanitizer has been applied, so that we can unit test
+    // the writer without it erroring.
+    SetTransformApplied<transform::Spirv>();
     [&]() {
       ASSERT_TRUE(IsValid()) << "Builder program is not valid\n"
                              << diag::Formatter().format(Diagnostics());