diff --git a/migrate_cpp/cpp_refactoring/fn_inserter.cpp b/migrate_cpp/cpp_refactoring/fn_inserter.cpp
index f175aa76ed14..17c44ab5bfcc 100644
--- a/migrate_cpp/cpp_refactoring/fn_inserter.cpp
+++ b/migrate_cpp/cpp_refactoring/fn_inserter.cpp
@@ -13,13 +13,8 @@ namespace Carbon {
 FnInserter::FnInserter(std::map<std::string, Replacements>& in_replacements,
                        cam::MatchFinder* finder)
     : Matcher(in_replacements) {
-  // TODO: Switch from isExpansionInMainFile to isDefinition. That should then
-  // include `for (const auto* redecl : func->redecls())` to generate
-  // replacements.
-  finder->addMatcher(
-      cam::functionDecl(cam::isExpansionInMainFile(), cam::hasTrailingReturn())
-          .bind(Label),
-      this);
+  finder->addMatcher(cam::functionDecl(cam::hasTrailingReturn()).bind(Label),
+                     this);
 }
 
 void FnInserter::run(const cam::MatchFinder::MatchResult& result) {
diff --git a/migrate_cpp/cpp_refactoring/main.cpp b/migrate_cpp/cpp_refactoring/main.cpp
index d0a50b3bf31f..93875875535b 100644
--- a/migrate_cpp/cpp_refactoring/main.cpp
+++ b/migrate_cpp/cpp_refactoring/main.cpp
@@ -9,11 +9,27 @@
 namespace cam = ::clang::ast_matchers;
 namespace ct = ::clang::tooling;
 
+// Initialize the files in replacements. Matcher will restrict replacements to
+// initialized files.
+static void InitReplacements(ct::RefactoringTool* tool) {
+  auto& files = tool->getFiles();
+  auto& repl = tool->getReplacements();
+  for (const auto& path : tool->getSourcePaths()) {
+    auto file = files.getFile(path);
+    if (file.getError()) {
+      llvm::report_fatal_error("Error accessing `" + path +
+                               "`: " + file.getError().message() + "\n");
+    }
+    repl.insert({files.getCanonicalName(*file).str(), {}});
+  }
+}
+
 auto main(int argc, const char** argv) -> int {
   llvm::cl::OptionCategory category("C++ refactoring options");
   auto parser = ct::CommonOptionsParser::create(argc, argv, category);
   ct::RefactoringTool tool(parser->getCompilations(),
                            parser->getSourcePathList());
+  InitReplacements(&tool);
 
   // Set up AST matcher callbacks.
   cam::MatchFinder finder;
diff --git a/migrate_cpp/cpp_refactoring/matcher.cpp b/migrate_cpp/cpp_refactoring/matcher.cpp
index e67fc13760c0..1b612cc39372 100644
--- a/migrate_cpp/cpp_refactoring/matcher.cpp
+++ b/migrate_cpp/cpp_refactoring/matcher.cpp
@@ -29,7 +29,14 @@ void Matcher::AddReplacement(const clang::SourceManager& sm,
   }
 
   auto rep = ct::Replacement(sm, sm.getExpansionRange(range), replacement_text);
-  auto err = (*replacements)[std::string(rep.getFilePath())].add(rep);
+  auto entry = replacements->find(std::string(rep.getFilePath()));
+  if (entry == replacements->end()) {
+    // The replacement was in a file which isn't being updated, such as a system
+    // header.
+    return;
+  }
+
+  auto err = entry->second.add(rep);
   if (err) {
     llvm::report_fatal_error("Error with replacement `" + rep.toString() +
                              "`: " + llvm::toString(std::move(err)) + "\n");
diff --git a/migrate_cpp/cpp_refactoring/matcher_test_base.cpp b/migrate_cpp/cpp_refactoring/matcher_test_base.cpp
index 57cc1153cbe1..0934f3f75b67 100644
--- a/migrate_cpp/cpp_refactoring/matcher_test_base.cpp
+++ b/migrate_cpp/cpp_refactoring/matcher_test_base.cpp
@@ -16,23 +16,20 @@ void MatcherTestBase::ExpectReplacement(llvm::StringRef before,
                                         llvm::StringRef after) {
   auto factory = ct::newFrontendActionFactory(&finder);
   constexpr char Filename[] = "test.cc";
+  replacements.clear();
+  replacements.insert({Filename, {}});
   ASSERT_TRUE(ct::runToolOnCodeWithArgs(
       factory->create(), before, {}, Filename, "clang-tool",
       std::make_shared<clang::PCHContainerOperations>(),
       ct::FileContentMappings()));
-  auto it = replacements.find(Filename);
-  if (it != replacements.end()) {
-    auto actual = ct::applyAllReplacements(before, it->second);
-    // Split lines to get gmock to get an easier-to-read error.
-    llvm::SmallVector<llvm::StringRef, 0> actual_lines;
-    llvm::SplitString(*actual, actual_lines, "\n");
-    llvm::SmallVector<llvm::StringRef, 0> after_lines;
-    llvm::SplitString(after, after_lines, "\n");
-    EXPECT_THAT(actual_lines, testing::ContainerEq(after_lines));
-  } else {
-    // No replacements; before and after should match.
-    EXPECT_THAT(before, testing::Eq(after));
-  }
+  EXPECT_THAT(replacements, testing::ElementsAre(testing::Key(Filename)));
+  auto actual = ct::applyAllReplacements(before, replacements[Filename]);
+  // Split lines to get gmock to get an easier-to-read error.
+  llvm::SmallVector<llvm::StringRef, 0> actual_lines;
+  llvm::SplitString(*actual, actual_lines, "\n");
+  llvm::SmallVector<llvm::StringRef, 0> after_lines;
+  llvm::SplitString(after, after_lines, "\n");
+  EXPECT_THAT(actual_lines, testing::ContainerEq(after_lines));
 }
 
 }  // namespace Carbon