Index: include-fixer/find-all-symbols/PathConfig.cpp
===================================================================
--- include-fixer/find-all-symbols/PathConfig.cpp
+++ include-fixer/find-all-symbols/PathConfig.cpp
@@ -33,7 +33,7 @@
   if (Collector)
     FilePath = Collector->getMappedHeader(FilePath);
   SmallString<256> CleanedFilePath = FilePath;
-  llvm::sys::path::remove_dots(CleanedFilePath, /*remove_dot_dot=*/true);
+  llvm::sys::path::remove_dots(CleanedFilePath, /*remove_dot_dot=*/false);
 
   return CleanedFilePath.str();
 }
Index: include-fixer/find-all-symbols/tool/FindAllSymbolsMain.cpp
===================================================================
--- include-fixer/find-all-symbols/tool/FindAllSymbolsMain.cpp
+++ include-fixer/find-all-symbols/tool/FindAllSymbolsMain.cpp
@@ -158,6 +158,5 @@
   auto Factory =
       llvm::make_unique<clang::find_all_symbols::FindAllSymbolsActionFactory>(
           &Reporter, clang::find_all_symbols::getSTLPostfixHeaderMap());
-  Tool.run(Factory.get());
-  return 0;
+  return Tool.run(Factory.get());
 }
Index: test/include-fixer/include_path.cpp
===================================================================
--- test/include-fixer/include_path.cpp
+++ test/include-fixer/include_path.cpp
@@ -1,14 +1,20 @@
 // REQUIRES: shell
 // RUN: mkdir -p %T/include-fixer/include
+// RUN: mkdir -p %T/include-fixer/symbols
 // RUN: mkdir -p %T/include-fixer/build
 // RUN: mkdir -p %T/include-fixer/src
 // RUN: sed 's|test_dir|%T/include-fixer|g' %S/Inputs/database_template.json > %T/include-fixer/build/compile_commands.json
-// RUN: cp %S/Inputs/fake_yaml_db.yaml %T/include-fixer/build/fake_yaml_db.yaml
-// RUN: echo 'b::a::bar f;' > %T/include-fixer/src/bar.cpp
-// RUN: touch %T/include-fixer/include/bar.h
+// RUN: echo -e '#include "bar.h"\nb::a::bar f;' > %T/include-fixer/src/bar.cpp
+// RUN: echo 'namespace b { namespace a { class bar {}; } }' > %T/include-fixer/include/bar.h
 // RUN: cd %T/include-fixer/build
-// RUN: clang-include-fixer -db=yaml -input=fake_yaml_db.yaml -p=. %T/include-fixer/src/bar.cpp
+// RUN: find-all-symbols -output-dir=%T/include-fixer/symbols -p=. %T/include-fixer/src/bar.cpp
+// RUN: find-all-symbols -merge-dir=%T/include-fixer/symbols %T/include-fixer/build/find_all_symbols.yaml
+// RUN: FileCheck -input-file=%T/include-fixer/build/find_all_symbols.yaml -check-prefix=CHECK-YAML %s
+//
+// RUN: echo 'b::a::bar f;' > %T/include-fixer/src/bar.cpp
+// RUN: clang-include-fixer -db=yaml -input=%T/include-fixer/build/find_all_symbols.yaml -p=. %T/include-fixer/src/bar.cpp
 // RUN: FileCheck -input-file=%T/include-fixer/src/bar.cpp %s
 
+// CHECK-YAML: ../include/bar.h
 // CHECK: #include "bar.h"
 // CHECK: b::a::bar f;
Index: unittests/include-fixer/find-all-symbols/FindAllSymbolsTests.cpp
===================================================================
--- unittests/include-fixer/find-all-symbols/FindAllSymbolsTests.cpp
+++ unittests/include-fixer/find-all-symbols/FindAllSymbolsTests.cpp
@@ -105,7 +105,7 @@
                           "#include \"internal/internal.h\"";
 #if !defined(_MSC_VER) && !defined(__MINGW32__)
     // Test path cleaning for both decls and macros.
-    const std::string DirtyHeader = "./internal/../internal/./a/b.h";
+    const std::string DirtyHeader = "./internal/./a/b.h";
     Content += "\n#include \"" + DirtyHeader + "\"";
     const std::string CleanHeader = "internal/a/b.h";
     const std::string DirtyHeaderContent =