diff --git a/src/clang_indexer.cc b/src/clang_indexer.cc
index 355cda29..cf36a4c1 100644
--- a/src/clang_indexer.cc
+++ b/src/clang_indexer.cc
@@ -1841,12 +1841,15 @@ void OnIndexReference(CXClientData client_data, const CXIdxEntityRefInfo* ref) {
       if (!ns.def.spell) {
         ClangCursor sem_parent = referenced.get_semantic_parent();
         ClangCursor lex_parent = referenced.get_lexical_parent();
-        ns.def.spell =
-            SetUse(db, referenced.get_spell(), sem_parent, Role::Definition);
-        ns.def.extent =
-            SetUse(db, referenced.get_extent(), lex_parent, Role::None);
-        std::string name = referenced.get_spell_name();
-        SetTypeName(ns, referenced, nullptr, name.c_str(), param);
+        CXFile referenced_file;
+        Range spell = referenced.get_spell(&referenced_file);
+        if (file == referenced_file) {
+          ns.def.spell = SetUse(db, spell, sem_parent, Role::Definition);
+          ns.def.extent =
+              SetUse(db, referenced.get_extent(), lex_parent, Role::None);
+          std::string name = referenced.get_spell_name();
+          SetTypeName(ns, referenced, nullptr, name.c_str(), param);
+        }
       }
       break;
     }
diff --git a/src/import_pipeline.cc b/src/import_pipeline.cc
index 14a341d2..680f3d67 100644
--- a/src/import_pipeline.cc
+++ b/src/import_pipeline.cc
@@ -71,6 +71,13 @@ bool Indexer_Parse(DiagnosticsEngine* diag_engine,
   auto& request = *opt_request;
   ICacheManager cache;
 
+  // dummy one to trigger refresh semantic highlight
+  if (request.path.empty()) {
+    queue->on_indexed.PushBack(
+        Index_OnIndexed(IndexUpdate{}, PerformanceImportFile()), false);
+    return false;
+  }
+
   Project::Entry entry;
   {
     std::lock_guard<std::mutex> lock(project->mutex_);
@@ -216,6 +223,18 @@ void QueryDb_OnIndexed(QueueManager* queue,
                        SemanticHighlightSymbolCache* semantic_cache,
                        WorkingFiles* working_files,
                        Index_OnIndexed* response) {
+
+  if (response->update.file_id < 0) { // dummy
+    LOG_S(INFO) << "Loaded project. Refresh semantic highlight for all working file.";
+    std::lock_guard<std::mutex> lock(working_files->files_mutex);
+    for (auto& f : working_files->files) {
+      int file_id = db->name2file_id[LowerPathIfInsensitive(f->filename)];
+      QueryFile* file = &db->files[file_id];
+      EmitSemanticHighlighting(db, semantic_cache, f.get(), file);
+    }
+    return;
+  }
+
   Timer time;
   db->ApplyIndexUpdate(&response->update);
 
diff --git a/src/include_complete.cc b/src/include_complete.cc
index f5ea1fc3..056a5b2b 100644
--- a/src/include_complete.cc
+++ b/src/include_complete.cc
@@ -106,8 +106,8 @@ void IncludeComplete::Rescan() {
     SetThreadName("scan_includes");
     Timer timer;
 
-    InsertIncludesFromDirectory(g_config->projectRoot,
-                                false /*use_angle_brackets*/);
+    // InsertIncludesFromDirectory(g_config->projectRoot,
+    //                             false /*use_angle_brackets*/);
     for (const std::string& dir : project_->quote_include_directories)
       InsertIncludesFromDirectory(dir, false /*use_angle_brackets*/);
     for (const std::string& dir : project_->angle_include_directories)
diff --git a/src/messages/initialize.cc b/src/messages/initialize.cc
index 9cbcba60..40571b8f 100644
--- a/src/messages/initialize.cc
+++ b/src/messages/initialize.cc
@@ -510,12 +510,9 @@ struct Handler_Initialize : BaseMessageHandler<In_InitializeRequest> {
       // Start indexer threads. Start this after loading the project, as that
       // may take a long time. Indexer threads will emit status/progress
       // reports.
-      if (g_config->index.threads == 0) {
-        // If the user has not specified how many indexers to run, try to
-        // guess an appropriate value. Default to 80% utilization.
-        g_config->index.threads =
-            std::max(int(std::thread::hardware_concurrency() * 0.8), 1);
-      }
+      if (g_config->index.threads == 0)
+        g_config->index.threads = std::thread::hardware_concurrency();
+
       LOG_S(INFO) << "Starting " << g_config->index.threads << " indexers";
       for (int i = 0; i < g_config->index.threads; i++) {
         std::thread([=]() {
diff --git a/src/project.cc b/src/project.cc
index d30e57e1..545f8cf8 100644
--- a/src/project.cc
+++ b/src/project.cc
@@ -563,6 +563,9 @@ void Project::Index(QueueManager* queue,
     queue->index_request.PushBack(Index_Request(entry.filename, entry.args,
                                                 is_interactive, *content, id));
   });
+  // dummy request to indicate that project is loaded and
+  // trigger refreshing semantic highlight for all working files
+  queue->index_request.PushBack(Index_Request("", {}, false, ""));
 }
 
 TEST_SUITE("Project") {
diff --git a/src/query.h b/src/query.h
index 51d96ef3..a146df9f 100644
--- a/src/query.h
+++ b/src/query.h
@@ -99,11 +99,7 @@ struct IndexUpdate {
   static IndexUpdate CreateDelta(IndexFile* previous,
                                  IndexFile* current);
 
-  // Merge |update| into this update; this can reduce overhead / index update
-  // work can be parallelized.
-  void Merge(IndexUpdate&& update);
-
-  int file_id;
+  int file_id = -1;
 
   // File updates.
   std::optional<std::string> files_removed;