diff --git a/foo/.vscode/settings.json b/foo/.vscode/settings.json
index 3cd417bf..7c74e0aa 100644
--- a/foo/.vscode/settings.json
+++ b/foo/.vscode/settings.json
@@ -1,5 +1,5 @@
 // Place your settings in this file to overwrite default and user settings.
 {
   "editor.lineNumbers": "on",
-  "cquery.cacheDirectory": "C:/Users/jacob/AppData/Roaming/Code/User/workspaceStorage/ff57708adc5718d939d7a59c9d5270c7/jacobdufault.cquery/cquerycache/"
+  "cquery.cacheDirectory": "C:/Users/jacob/Desktop/superindex/indexer/CACHE"
 }
\ No newline at end of file
diff --git a/foo/_empty_test.cc b/foo/_empty_test.cc
deleted file mode 100644
index d3b3f523..00000000
--- a/foo/_empty_test.cc
+++ /dev/null
@@ -1,35 +0,0 @@
-#if false
-#include <string>
-#include <vector>
-
-struct MyBar {
-  int x;
-  int aaaa1;
-  int aaaa2;
-  int aaaa3;
-  static int foobez;
-
-  // This is some awesome docs.
-  float MemberFunc(int a, char b, std::vector<int> foo);
-  float MemberFunc2(int a, char b, std::vector<int> foo);
-
-  // The names are some extra state.
-  std::vector<std::string> names;
-};
-
-int MyBar::foobez;
-
-int foo() {
-  int a = 10;
-  MyBar foooo;
-  MyBar f;
-  MyBar f2;
-}
-
-float MyBar::MemberFunc(int a, char b, std::vector<int> foo) {
-  this->x = 100;
-  this->MemberFunc(0, 0, {});
-
-  return ::foo();
-}
-#endif
\ No newline at end of file
diff --git a/foo/a.cc b/foo/a.cc
deleted file mode 100644
index 928c8ff1..00000000
--- a/foo/a.cc
+++ /dev/null
@@ -1,111 +0,0 @@
-#if false
-/*
-abc
-daaa
-faf
-dakkdakk
-abaa
-*/
-#include <string>
-
-#include "a.h"
-
-
-struct iface {
-  virtual void foo() = 0;
-};
-struct impl : public iface {
-  void foo() override {}
-};
-
-void doit() {
-  iface* f;
-  f->foo();
-}
-
-struct Middle : public Parent {
-  void foo() override {}
-};
-struct DerivedA : public Middle {
-  void foo() override {}
-};
-struct DerivedB : public Middle {
-  void foo() override {}
-};
-struct Derived2B : public DerivedB {
-  void foo() override {}
-};
-
-struct Derived2C : public DerivedB {
-  void foo() override;
-};
-
-
-void Derived2C::foo() {}
-
-void User() {
-  Parent p;
-  Middle m;
-  DerivedA da;
-  DerivedB db;
-  Derived2B d2b;
-
-  p.foo();
-  m.foo();
-  da.foo();
-  db.foo();
-  d2b.foo();
-}
-
-
-
-
-
-struct Saaaaaa {};
-
-struct S2 {
-  S2() {}
-
-  int a;
-  int b;
-};
-
-struct MyFoo {
-  std::string name;
-};
-
-void f() {
-  S2 s2;
-  s2.a += 10;
-  s2.b -= 100;
-  s2.b -= 5;
-
-  MyFoo f;
-  // f.name = 10;
-  f.name = "okay";
-
-  MyFoo f2;
-  f2.name = "yes!";
-}
-
-
-void baz();
-
-void foo();
-void foo();
-
-void foo() {}
-
-/**/
-void caller() {
-  MyFoo fff;
-  fff.name = "this name";
-  baz();
-  baz();
-  baz();
-  foo();
-
-  foo();
-  foo();
-}
-#endif
\ No newline at end of file
diff --git a/foo/a.h b/foo/a.h
index cd6e7b7f..1db6b5e0 100644
--- a/foo/a.h
+++ b/foo/a.h
@@ -1 +1,3 @@
-a,b,c
\ No newline at end of file
+
+
+void foobar() {}
\ No newline at end of file
diff --git a/foo/b.cc b/foo/b.cc
index 2c226e7f..7038852a 100644
--- a/foo/b.cc
+++ b/foo/b.cc
@@ -1,4 +1,8 @@
+#include "a.h"
 
 enum Foo {
-  #include "a.h"
-};
\ No newline at end of file
+};
+
+void faz() {
+  foobar();
+}
\ No newline at end of file
diff --git a/src/command_line.cc b/src/command_line.cc
index c254da56..0045fee2 100644
--- a/src/command_line.cc
+++ b/src/command_line.cc
@@ -896,7 +896,7 @@ bool IndexMain_DoIndex(IndexerConfig* config,
         queue_do_index->PriorityEnqueue(std::move(dep_index_request));
       }
       
-      project->UpdateModificationTime(index_request->path, old_index->last_modification_time);
+      project->UpdateFileState(index_request->path, old_index->import_file, old_index->last_modification_time);
 
       Index_DoIdMap response(nullptr, std::move(old_index));
       queue_do_id_map->Enqueue(std::move(response));
@@ -912,10 +912,13 @@ bool IndexMain_DoIndex(IndexerConfig* config,
   }
 
   // Parse request and send a response.
+  std::string import_file = index_request->path;
 
   // Skip index if file modification time didn't change.
   optional<Project::Entry> entry = project->FindCompilationEntryForFile(index_request->path);
   if (entry && entry->last_modification_time) {
+    import_file = entry->import_file;
+
     int64_t modification_time = GetLastModificationTime(index_request->path);
     if (modification_time == *entry->last_modification_time) {
       time.ResetAndPrint("Skipping index update on " + index_request->path + " since file modification time has not changed");
@@ -923,12 +926,14 @@ bool IndexMain_DoIndex(IndexerConfig* config,
     }
   }
 
-  std::vector<std::unique_ptr<IndexedFile>> indexes = Parse(config, file_consumer_shared, index_request->path, index_request->args);
+  std::vector<std::unique_ptr<IndexedFile>> indexes = Parse(config, file_consumer_shared, index_request->path, import_file, index_request->args);
   time.ResetAndPrint("Parsing/indexing " + index_request->path);
 
   for (auto& current_index : indexes) {
     std::cerr << "Got index for " << current_index->path << std::endl;
 
+    project->UpdateFileState(current_index->path, current_index->import_file, current_index->last_modification_time);
+
     std::unique_ptr<IndexedFile> old_index = LoadCachedFile(config, current_index->path);
     time.ResetAndPrint("Loading cached index");
 
diff --git a/src/indexer.cc b/src/indexer.cc
index fa02e8d0..e38722d4 100644
--- a/src/indexer.cc
+++ b/src/indexer.cc
@@ -192,6 +192,9 @@ struct IndexParam {
   // Only use this when strictly needed (ie, primary translation unit is
   // needed). Most logic should get the IndexedFile instance via
   // |file_consumer|.
+  //
+  // This can be null if we're not generating an index for the primary
+  // translation unit.
   IndexedFile* primary_file;
 
   FileConsumer* file_consumer;
@@ -698,7 +701,7 @@ void indexDeclaration(CXClientData client_data, const CXIdxDeclInfo* decl) {
   if (!db)
     return;
 
-  if (is_first_time_visiting_file)
+  if (is_first_time_visiting_file && param->primary_file)
     param->primary_file->dependencies.push_back(db->path);
 
   NamespaceHelper* ns = &param->ns;
@@ -1156,7 +1159,7 @@ void indexEntityReference(CXClientData client_data,
   if (!db)
     return;
 
-  if (is_first_time_visiting_file)
+  if (is_first_time_visiting_file && param->primary_file)
     param->primary_file->dependencies.push_back(db->path);
 
   // ref->cursor mainFile=0
@@ -1332,17 +1335,21 @@ void indexEntityReference(CXClientData client_data,
 
 
 
+std::vector<std::unique_ptr<IndexedFile>> Parse(
+    IndexerConfig* config, FileConsumer::SharedState* file_consumer_shared,
+    std::string desired_index_file, std::string import_file, std::vector<std::string> args,
+    bool dump_ast) {
 
-std::vector<std::unique_ptr<IndexedFile>> Parse(IndexerConfig* config, FileConsumer::SharedState* file_consumer_shared, std::string filename, std::vector<std::string> args, bool dump_ast) {
   if (!config->enableIndexing)
     return {};
 
-  filename = NormalizePath(filename);
+  desired_index_file = NormalizePath(desired_index_file);
+  import_file = NormalizePath(import_file);
 
   clang::Index index(0 /*excludeDeclarationsFromPCH*/,
                      0 /*displayDiagnostics*/);
   std::vector<CXUnsavedFile> unsaved_files;
-  clang::TranslationUnit tu(config, index, filename, args, unsaved_files, CXTranslationUnit_KeepGoing);
+  clang::TranslationUnit tu(config, index, import_file, args, unsaved_files, CXTranslationUnit_KeepGoing);
 
   if (dump_ast)
     Dump(tu.document_cursor());
@@ -1357,16 +1364,21 @@ std::vector<std::unique_ptr<IndexedFile>> Parse(IndexerConfig* config, FileConsu
   FileConsumer file_consumer(file_consumer_shared);
   IndexParam param(&file_consumer);
 
-  CXFile file = clang_getFile(tu.cx_tu, filename.c_str());
+  CXFile file = clang_getFile(tu.cx_tu, desired_index_file.c_str());
   param.primary_file = file_consumer.ForceLocal(file);
+  if (desired_index_file != import_file)
+    param.primary_file = nullptr;
 
-  std::cerr << "!! [START] Indexing " << filename << std::endl;
+  if (desired_index_file != import_file)
+    std::cerr << "!! [START] Indexing desired_index_file=" << desired_index_file << ", import_file=" << import_file << std::endl;
+  else
+    std::cerr << "!! [START] Indexing " << desired_index_file << std::endl;
   CXIndexAction index_action = clang_IndexAction_create(index.cx_index);
   clang_indexTranslationUnit(index_action, &param, callbacks, sizeof(callbacks),
                              CXIndexOpt_IndexFunctionLocalSymbols | CXIndexOpt_SkipParsedBodiesInSession | CXIndexOpt_IndexImplicitTemplateInstantiations,
                              tu.cx_tu);
   clang_IndexAction_dispose(index_action);
-  std::cerr << "!! [END] Indexing " << filename << std::endl;
+  std::cerr << "!! [END] Indexing " << desired_index_file << std::endl;
 
   auto result = param.file_consumer->TakeLocalState();
   for (auto& entry : result) {
@@ -1378,27 +1390,28 @@ std::vector<std::unique_ptr<IndexedFile>> Parse(IndexerConfig* config, FileConsu
     entry->id_cache.primary_file = entry->path;
 
     entry->last_modification_time = GetLastModificationTime(entry->path);
+    entry->import_file = import_file;
   }
 
   // TODO: Fix interesting checks.
   for (auto& entry : result) {
     for (auto& type : entry->types) {
       if (!type.HasInterestingState()) {
-        std::cerr << "!!!! NO INTERESTING STATE FOR " << entry->path << " of !!! " << filename << std::endl;
+        std::cerr << "!!!! NO INTERESTING STATE FOR " << entry->path << " of !!! " << desired_index_file << std::endl;
         std::cerr << "!!!! USR " << type.def.usr << std::endl;
         assert(false);
       }
     }
     for (auto& func : entry->funcs) {
       if (!func.HasInterestingState()) {
-        std::cerr << "!!!! NO INTERESTING STATE FOR " << entry->path << " of !!! " << filename << std::endl;
+        std::cerr << "!!!! NO INTERESTING STATE FOR " << entry->path << " of !!! " << desired_index_file << std::endl;
         std::cerr << "!!!! USR " << func.def.usr << std::endl;
         assert(false);
       }
     }
     for (auto& var : entry->vars) {
       if (!var.HasInterestingState()) {
-        std::cerr << "!!!! NO INTERESTING STATE FOR " << entry->path << " of !!! " << filename << std::endl;
+        std::cerr << "!!!! NO INTERESTING STATE FOR " << entry->path << " of !!! " << desired_index_file << std::endl;
         std::cerr << "!!!! USR " << var.def.usr << std::endl;
         assert(false);
       }
diff --git a/src/indexer.h b/src/indexer.h
index 100eb821..2ca728a8 100644
--- a/src/indexer.h
+++ b/src/indexer.h
@@ -471,6 +471,12 @@ struct IndexedFile {
   std::string path;
   int64_t last_modification_time = 0;
 
+  // The path to the translation unit cc file which caused the creation of this
+  // IndexedFile. When parsing a translation unit we generate many IndexedFile
+  // instances (ie, each header has a separate one). When the user edits a
+  // header we need to lookup the original translation unit and reindex that.
+  std::string import_file;
+
   // The content of |path| when it was indexed.
   //std::string content;
 
@@ -494,5 +500,10 @@ struct IndexedFile {
   std::string ToString();
 };
 
-std::vector<std::unique_ptr<IndexedFile>> Parse(IndexerConfig* config, FileConsumer::SharedState* file_consumer_shared, std::string filename, std::vector<std::string> args, bool dump_ast = false);
+// |import_file| is the cc file which is what gets passed to clang.
+// |desired_index_file| is the (h or cc) file which has actually changed.
+std::vector<std::unique_ptr<IndexedFile>> Parse(
+    IndexerConfig* config, FileConsumer::SharedState* file_consumer_shared,
+    std::string desired_index_file, std::string import_file, std::vector<std::string> args,
+    bool dump_ast = false);
 void IndexInit();
diff --git a/src/libclangmm/TranslationUnit.cc b/src/libclangmm/TranslationUnit.cc
index 4313e4c5..e84257fc 100644
--- a/src/libclangmm/TranslationUnit.cc
+++ b/src/libclangmm/TranslationUnit.cc
@@ -28,12 +28,10 @@ TranslationUnit::TranslationUnit(
   for (const std::string& arg : config->extraClangArguments)
     args.push_back(arg.c_str());
 
-#if false
   std::cerr << "Parsing " << filepath << " with args ";
   for (const auto& arg : args)
     std::cerr << arg << " ";
   std::cerr << std::endl;
-#endif
 
   CXErrorCode error_code = clang_parseTranslationUnit2(
     index.cx_index,
diff --git a/src/project.cc b/src/project.cc
index 9420bdcf..65b6e9ac 100644
--- a/src/project.cc
+++ b/src/project.cc
@@ -250,6 +250,7 @@ void Project::Load(const std::string& directory) {
 }
 
 optional<Project::Entry> Project::FindCompilationEntryForFile(const std::string& filename) {
+  // TODO: There might be a lot of thread contention here.
   std::lock_guard<std::mutex> lock(entries_modification_mutex_);
 
   auto it = absolute_path_to_entry_index_.find(filename);
@@ -258,19 +259,32 @@ optional<Project::Entry> Project::FindCompilationEntryForFile(const std::string&
   return nullopt;
 }
 
-void Project::UpdateModificationTime(const std::string& filename, uint64_t modification_time) {
-  // TODO: There might be a lot of thread contention here.
-  std::lock_guard<std::mutex> lock(entries_modification_mutex_);
-
-  auto it = absolute_path_to_entry_index_.find(filename);
-  if (it != absolute_path_to_entry_index_.end()) {
-    entries[it->second].last_modification_time = modification_time;
+void Project::UpdateFileState(const std::string& filename, const std::string& import_file, uint64_t modification_time) {
+  {
+    // TODO: There might be a lot of thread contention here.
+    std::lock_guard<std::mutex> lock(entries_modification_mutex_);
+    auto it = absolute_path_to_entry_index_.find(filename);
+    if (it != absolute_path_to_entry_index_.end()) {
+      auto& entry = entries[it->second];
+      entry.import_file = import_file;
+      entry.last_modification_time = modification_time;
+      return;
+    }
   }
-  else {
+
+  {
+    optional<Project::Entry> import_entry = FindCompilationEntryForFile(import_file);
+
     Project::Entry entry;
     entry.filename = filename;
-    entry.last_modification_time = modification_time;
+    if (import_entry)
+      entry.args = import_entry->args;
 
+    entry.import_file = import_file;
+    entry.last_modification_time = modification_time;
+    
+    // TODO: There might be a lot of thread contention here.
+    std::lock_guard<std::mutex> lock(entries_modification_mutex_);
     absolute_path_to_entry_index_[filename] = entries.size();
     entries.push_back(entry);
   }
diff --git a/src/project.h b/src/project.h
index b71d520d..3727ed76 100644
--- a/src/project.h
+++ b/src/project.h
@@ -14,6 +14,8 @@ struct Project {
   struct Entry {
     std::string filename;
     std::vector<std::string> args;
+    
+    std::string import_file;
     optional<uint64_t> last_modification_time;
   };
 
@@ -33,6 +35,6 @@ struct Project {
   optional<Entry> FindCompilationEntryForFile(const std::string& filename);
 
   // Update the modification time for the given filename. This is thread-safe.
-  void UpdateModificationTime(const std::string& filename, uint64_t modification_time);
+  void UpdateFileState(const std::string& filename, const std::string& import_file, uint64_t modification_time);
 };
 
diff --git a/src/serializer.cc b/src/serializer.cc
index 440e4a9c..c990e291 100644
--- a/src/serializer.cc
+++ b/src/serializer.cc
@@ -229,6 +229,7 @@ void Reflect(TVisitor& visitor, IndexedFile& value) {
   if (!gTestOutputMode) {
     REFLECT_MEMBER(version);
     REFLECT_MEMBER(last_modification_time);
+    REFLECT_MEMBER(import_file);
   }
   REFLECT_MEMBER(dependencies);
   REFLECT_MEMBER(types);
diff --git a/src/test.cc b/src/test.cc
index cabd727e..5abfe7ce 100644
--- a/src/test.cc
+++ b/src/test.cc
@@ -137,14 +137,18 @@ void RunTests() {
 
     // Run test.
     std::cout << "[START] " << path << std::endl;
-    std::vector<std::unique_ptr<IndexedFile>> dbs = Parse(&config, &file_consumer_shared, path, {
-        "-xc++",
-        "-std=c++11",
-        "-IC:/Users/jacob/Desktop/superindex/indexer/third_party/",
-        "-IC:/Users/jacob/Desktop/superindex/indexer/third_party/doctest/",
-        "-IC:/Users/jacob/Desktop/superindex/indexer/third_party/rapidjson/include",
-        "-IC:/Users/jacob/Desktop/superindex/indexer/src"
-    }, false /*dump_ast*/);
+    std::vector<std::unique_ptr<IndexedFile>> dbs = Parse(
+        &config, &file_consumer_shared,
+        path, path,
+        {
+          "-xc++",
+          "-std=c++11",
+          "-IC:/Users/jacob/Desktop/superindex/indexer/third_party/",
+          "-IC:/Users/jacob/Desktop/superindex/indexer/third_party/doctest/",
+          "-IC:/Users/jacob/Desktop/superindex/indexer/third_party/rapidjson/include",
+          "-IC:/Users/jacob/Desktop/superindex/indexer/src"
+        },
+        false /*dump_ast*/);
 
 #if false
     for (auto& db : dbs) {