diff --git a/src/match.cc b/src/match.cc
index 94499b67..40393a8e 100644
--- a/src/match.cc
+++ b/src/match.cc
@@ -41,7 +41,7 @@ optional<Matcher> Matcher::Create(const std::string& search) {
 bool Matcher::IsMatch(const std::string& value) const {
   // std::smatch match;
   // return std::regex_match(value, match, regex);
-  return std::regex_match(value, regex, std::regex_constants::match_any);
+  return std::regex_search(value, regex, std::regex_constants::match_any);
 }
 
 GroupMatch::GroupMatch(const std::vector<std::string>& whitelist,
diff --git a/src/messages/cquery_freshen_index.cc b/src/messages/cquery_freshen_index.cc
index 32b72c87..a75334a4 100644
--- a/src/messages/cquery_freshen_index.cc
+++ b/src/messages/cquery_freshen_index.cc
@@ -8,14 +8,21 @@
 #include "working_files.h"
 
 #include <loguru.hpp>
+#include <queue>
+#include <unordered_set>
 
 namespace {
-struct Ipc_CqueryFreshenIndex : public RequestMessage<Ipc_CqueryFreshenIndex> {
+struct Ipc_CqueryFreshenIndex : public NotificationMessage<Ipc_CqueryFreshenIndex> {
   const static IpcId kIpcId = IpcId::CqueryFreshenIndex;
-  std::vector<std::string> whitelist;
-  std::vector<std::string> blacklist;
+  struct Params {
+    bool dependencies = true;
+    std::vector<std::string> whitelist;
+    std::vector<std::string> blacklist;
+  };
+  Params params;
 };
-MAKE_REFLECT_STRUCT(Ipc_CqueryFreshenIndex, id, whitelist, blacklist);
+MAKE_REFLECT_STRUCT(Ipc_CqueryFreshenIndex::Params, dependencies, whitelist, blacklist);
+MAKE_REFLECT_STRUCT(Ipc_CqueryFreshenIndex, params);
 REGISTER_IPC_MESSAGE(Ipc_CqueryFreshenIndex);
 
 struct CqueryFreshenIndexHandler : BaseMessageHandler<Ipc_CqueryFreshenIndex> {
@@ -23,24 +30,52 @@ struct CqueryFreshenIndexHandler : BaseMessageHandler<Ipc_CqueryFreshenIndex> {
     LOG_S(INFO) << "Freshening " << project->entries.size() << " files";
 
     // TODO: think about this flow and test it more.
-    GroupMatch matcher(request->whitelist, request->blacklist);
+    GroupMatch matcher(request->params.whitelist, request->params.blacklist);
 
     // Unmark all files whose timestamp has changed.
     std::unique_ptr<ICacheManager> cache_manager = ICacheManager::Make(config);
-    for (const auto& file : db->files) {
-      if (!file.def || !matcher.IsMatch(file.def->path))
-        continue;
+
+    std::queue<const QueryFile*> q;
+    // |need_index| stores every filename ever enqueued.
+    std::unordered_set<std::string> need_index;
+    // Reverse dependency graph.
+    std::unordered_map<std::string, std::vector<std::string>> graph;
+    // filename -> QueryFile mapping for files haven't enqueued.
+    std::unordered_map<std::string, const QueryFile*> path_to_file;
+
+    for (const auto& file : db->files)
+      if (file.def) {
+        if (matcher.IsMatch(file.def->path))
+          q.push(&file);
+        else
+          path_to_file[file.def->path] = &file;
+        for (const std::string& dependency : file.def->dependencies)
+          graph[dependency].push_back(file.def->path);
+      }
+
+    while (!q.empty()) {
+      const QueryFile* file = q.front();
+      q.pop();
+      need_index.insert(file->def->path);
 
       optional<int64_t> modification_timestamp =
-          GetLastModificationTime(file.def->path);
+          GetLastModificationTime(file->def->path);
       if (!modification_timestamp)
         continue;
-
       optional<int64_t> cached_modification =
           timestamp_manager->GetLastCachedModificationTime(cache_manager.get(),
-                                                           file.def->path);
+                                                           file->def->path);
       if (modification_timestamp != cached_modification)
-        file_consumer_shared->Reset(file.def->path);
+        file_consumer_shared->Reset(file->def->path);
+
+      if (request->params.dependencies)
+        for (const std::string& path : graph[file->def->path]) {
+          auto it = path_to_file.find(path);
+          if (it != path_to_file.end()) {
+            q.push(it->second);
+            path_to_file.erase(it);
+          }
+        }
     }
 
     auto* queue = QueueManager::instance();
@@ -48,7 +83,7 @@ struct CqueryFreshenIndexHandler : BaseMessageHandler<Ipc_CqueryFreshenIndex> {
     // Send index requests for every file.
     project->ForAllFilteredFiles(
         config, [&](int i, const Project::Entry& entry) {
-          if (!matcher.IsMatch(entry.filename))
+          if (!need_index.count(entry.filename))
             return;
           optional<std::string> content = ReadContent(entry.filename);
           if (!content) {
diff --git a/src/query.cc b/src/query.cc
index 659bb4b6..ea4aaa8b 100644
--- a/src/query.cc
+++ b/src/query.cc
@@ -201,6 +201,7 @@ QueryFile::Def BuildFileDef(const IdMap& id_map, const IndexFile& indexed) {
   def.path = indexed.path;
   def.includes = indexed.includes;
   def.inactive_regions = indexed.skipped_by_preprocessor;
+  def.dependencies = indexed.dependencies;
 
   // Convert enum to markdown compatible strings
   def.language = [indexed]() {
diff --git a/src/query.h b/src/query.h
index 38d4ce6b..d2e4e69f 100644
--- a/src/query.h
+++ b/src/query.h
@@ -192,6 +192,8 @@ struct QueryFile {
     std::vector<SymbolRef> all_symbols;
     // Parts of the file which are disabled.
     std::vector<Range> inactive_regions;
+    // Used by |$cquery/freshenIndex|.
+    std::vector<std::string> dependencies;
   };
 
   using DefUpdate = Def;
@@ -209,7 +211,8 @@ MAKE_REFLECT_STRUCT(QueryFile::Def,
                     language,
                     outline,
                     all_symbols,
-                    inactive_regions);
+                    inactive_regions,
+                    dependencies);
 
 struct QueryType {
   using Def = TypeDefDefinitionData<QueryTypeId,