diff --git a/src/command_line.cc b/src/command_line.cc
index f4519337..0fbd2a3a 100644
--- a/src/command_line.cc
+++ b/src/command_line.cc
@@ -20,6 +20,7 @@
 #include "test.h"
 #include "timer.h"
 #include "threaded_queue.h"
+#include "work_thread.h"
 #include "working_files.h"
 
 #include <loguru.hpp>
@@ -189,7 +190,7 @@ bool FindFileOrFail(QueryDatabase* db, lsRequestId id, const std::string& absolu
   if (out_file_id)
     *out_file_id = QueryFileId((size_t)-1);
 
-  LOG_S(INFO) << "Unable to find file " << absolute_path;
+  LOG_S(INFO) << "Unable to find file \"" << absolute_path << "\"";
 
   Out_Error out;
   out.id = id;
@@ -541,9 +542,10 @@ struct Index_Request {
   std::string path;
   std::vector<std::string> args; // TODO: make this a string that is parsed lazily.
   bool is_interactive;
+  optional<std::string> contents; // Preloaded contents. Useful for tests.
 
-  Index_Request(const std::string& path, const std::vector<std::string>& args, bool is_interactive)
-    : path(path), args(args), is_interactive(is_interactive) {}
+  Index_Request(const std::string& path, const std::vector<std::string>& args, bool is_interactive, optional<std::string> contents)
+    : path(path), args(args), is_interactive(is_interactive), contents(contents) {}
 };
 
 struct Index_DoIdMap {
@@ -652,6 +654,15 @@ struct QueueManager {
   Index_OnIndexedQueue on_indexed;
 
   QueueManager(MultiQueueWaiter* waiter) : index_request(waiter), do_id_map(waiter), load_previous_index(waiter), on_id_mapped(waiter), on_indexed(waiter) {}
+
+  bool HasWork() {
+    return
+        !index_request.IsEmpty() ||
+        !do_id_map.IsEmpty() ||
+        !load_previous_index.IsEmpty() ||
+        !on_id_mapped.IsEmpty() ||
+        !on_indexed.IsEmpty();
+  }
 };
 
 void RegisterMessageTypes() {
@@ -684,6 +695,9 @@ void RegisterMessageTypes() {
   MessageRegistry::instance()->Register<Ipc_CqueryCallers>();
   MessageRegistry::instance()->Register<Ipc_CqueryBase>();
   MessageRegistry::instance()->Register<Ipc_CqueryDerived>();
+  MessageRegistry::instance()->Register<Ipc_CqueryIndexFile>();
+  MessageRegistry::instance()->Register<Ipc_CqueryQueryDbWaitForIdleIndexer>();
+  MessageRegistry::instance()->Register<Ipc_CqueryExitWhenIdle>();
 }
 
 
@@ -726,6 +740,12 @@ struct ImportManager {
     import_.erase(path);
   }
 
+  // Returns true if there any any files currently being imported.
+  bool HasActiveImports() {
+    std::lock_guard<std::mutex> guard(mutex_);
+    return !import_.empty();
+  }
+
   std::mutex mutex_;
   std::unordered_set<std::string> import_;
 };
@@ -832,7 +852,8 @@ std::vector<Index_DoIdMap> DoParseFile(
     CacheLoader* cache_loader,
     bool is_interactive,
     const std::string& path,
-    const std::vector<std::string>& args) {
+    const std::vector<std::string>& args,
+    const optional<FileContents>& contents) {
   std::vector<Index_DoIdMap> result;
 
   IndexFile* previous_index = cache_loader->TryLoad(path);
@@ -904,6 +925,10 @@ std::vector<Index_DoIdMap> DoParseFile(
   //       well. We then default to a fast file-copy if not in working set.
   bool loaded_primary = false;
   std::vector<FileContents> file_contents;
+  if (contents) {
+    loaded_primary = loaded_primary || contents->path == path;
+    file_contents.push_back(*contents);
+  }
   for (const auto& it : cache_loader->caches) {
     const std::unique_ptr<IndexFile>& index = it.second;
     assert(index);
@@ -930,6 +955,7 @@ std::vector<Index_DoIdMap> DoParseFile(
     config, file_consumer_shared,
     path, args, file_contents,
     &perf, index);
+  // LOG_S(INFO) << "Parsing " << path << " gave " << indexes.size() << " indexes";
 
   for (std::unique_ptr<IndexFile>& new_index : indexes) {
     Timer time;
@@ -964,7 +990,12 @@ std::vector<Index_DoIdMap> ParseFile(
     FileConsumer::SharedState* file_consumer_shared,
     TimestampManager* timestamp_manager,
     bool is_interactive,
-    const Project::Entry& entry) {
+    const Project::Entry& entry,
+    const optional<std::string>& contents) {
+
+  optional<FileContents> file_contents;
+  if (contents)
+    file_contents = FileContents(entry.filename, *contents);
 
   CacheLoader cache_loader(config);
 
@@ -973,7 +1004,7 @@ std::vector<Index_DoIdMap> ParseFile(
   // complain about if indexed by itself.
   IndexFile* entry_cache = cache_loader.TryLoad(entry.filename);
   std::string tu_path = entry_cache ? entry_cache->import_file : entry.filename;
-  return DoParseFile(config, working_files, index, file_consumer_shared, timestamp_manager, &cache_loader, is_interactive, tu_path, entry.args);
+  return DoParseFile(config, working_files, index, file_consumer_shared, timestamp_manager, &cache_loader, is_interactive, tu_path, entry.args, file_contents);
 }
 
 bool IndexMain_DoParse(
@@ -985,18 +1016,28 @@ bool IndexMain_DoParse(
     TimestampManager* timestamp_manager,
     clang::Index* index) {
 
-  optional<Index_Request> request = queue->index_request.TryDequeue();
-  if (!request)
-    return false;
-
-  if (!import_manager->StartImport(request->path))
+  bool can_import = false;
+  optional<Index_Request> request = queue->index_request.TryDequeuePlusAction([&](const Index_Request& request) {
+    can_import = import_manager->StartImport(request.path);
+  });
+  if (!request || !can_import)
     return false;
 
   Project::Entry entry;
   entry.filename = request->path;
   entry.args = request->args;
-  std::vector<Index_DoIdMap> responses = ParseFile(config, working_files, index, file_consumer_shared, timestamp_manager, request->is_interactive, entry);
+  std::vector<Index_DoIdMap> responses = ParseFile(config, working_files, index, file_consumer_shared, timestamp_manager, request->is_interactive, entry, request->contents);
 
+  // Unmark file as imported if indexing failed.
+  bool found_import = false;
+  for (auto& response : responses) {
+    if (response.current->path == request->path)
+      found_import = true;
+  }
+  if (!found_import)
+    import_manager->DoneImport(request->path);
+
+  // Don't bother sending an IdMap request if there are no responses.
   if (responses.empty())
     return false;
 
@@ -1100,48 +1141,48 @@ bool IndexMergeIndexUpdates(QueueManager* queue) {
   }
 }
 
-void IndexMain(Config* config,
-               FileConsumer::SharedState* file_consumer_shared,
-               ImportManager* import_manager,
-               TimestampManager* timestamp_manager,
-               Project* project,
-               WorkingFiles* working_files,
-               MultiQueueWaiter* waiter,
-               QueueManager* queue) {
-  SetCurrentThreadName("indexer");
+WorkThread::Result IndexMain(
+    Config* config,
+    FileConsumer::SharedState* file_consumer_shared,
+    ImportManager* import_manager,
+    TimestampManager* timestamp_manager,
+    Project* project,
+    WorkingFiles* working_files,
+    MultiQueueWaiter* waiter,
+    QueueManager* queue) {
   // TODO: dispose of index after it is not used for a while.
   clang::Index index(1, 0);
 
-  while (true) {
-    // TODO: process all off IndexMain_DoIndex before calling
-    // IndexMain_DoCreateIndexUpdate for
-    //       better icache behavior. We need to have some threads spinning on
-    //       both though
-    //       otherwise memory usage will get bad.
+  // TODO: process all off IndexMain_DoIndex before calling
+  // IndexMain_DoCreateIndexUpdate for
+  //       better icache behavior. We need to have some threads spinning on
+  //       both though
+  //       otherwise memory usage will get bad.
 
-    // We need to make sure to run both IndexMain_DoParse and
-    // IndexMain_DoCreateIndexUpdate so we don't starve querydb from doing any
-    // work. Running both also lets the user query the partially constructed
-    // index.
-    bool did_parse = IndexMain_DoParse(config, working_files, queue, file_consumer_shared, import_manager, timestamp_manager, &index);
+  // We need to make sure to run both IndexMain_DoParse and
+  // IndexMain_DoCreateIndexUpdate so we don't starve querydb from doing any
+  // work. Running both also lets the user query the partially constructed
+  // index.
+  bool did_parse = IndexMain_DoParse(config, working_files, queue, file_consumer_shared, import_manager, timestamp_manager, &index);
 
-    bool did_create_update =
-        IndexMain_DoCreateIndexUpdate(config, queue, timestamp_manager);
+  bool did_create_update =
+      IndexMain_DoCreateIndexUpdate(config, queue, timestamp_manager);
 
-    bool did_load_previous = IndexMain_LoadPreviousIndex(config, queue);
+  bool did_load_previous = IndexMain_LoadPreviousIndex(config, queue);
 
-    // Nothing to index and no index updates to create, so join some already
-    // created index updates to reduce work on querydb thread.
-    bool did_merge = false;
-    if (!did_parse && !did_create_update && !did_load_previous)
-      did_merge = IndexMergeIndexUpdates(queue);
+  // Nothing to index and no index updates to create, so join some already
+  // created index updates to reduce work on querydb thread.
+  bool did_merge = false;
+  if (!did_parse && !did_create_update && !did_load_previous)
+    did_merge = IndexMergeIndexUpdates(queue);
 
-    // We didn't do any work, so wait for a notification.
-    if (!did_parse && !did_create_update && !did_merge && !did_load_previous) {
-      waiter->Wait(
-          {&queue->index_request, &queue->on_id_mapped, &queue->load_previous_index, &queue->on_indexed});
-    }
+  // We didn't do any work, so wait for a notification.
+  if (!did_parse && !did_create_update && !did_merge && !did_load_previous) {
+    waiter->Wait(
+        {&queue->index_request, &queue->on_id_mapped, &queue->load_previous_index, &queue->on_indexed});
   }
+
+  return queue->HasWork() ? WorkThread::Result::MoreWork : WorkThread::Result::NoWork;
 }
 
 bool QueryDb_ImportMain(Config* config, QueryDatabase* db, ImportManager* import_manager, QueueManager* queue, WorkingFiles* working_files) {
@@ -1157,8 +1198,8 @@ bool QueryDb_ImportMain(Config* config, QueryDatabase* db, ImportManager* import
     // it, load the previous state from disk and rerun IdMap logic later. Do not
     // do this if we have already attempted in the past.
     if (!request->load_previous &&
-      !request->previous &&
-      db->usr_to_file.find(LowerPathIfCaseInsensitive(request->current->path)) != db->usr_to_file.end()) {
+        !request->previous &&
+        db->usr_to_file.find(LowerPathIfCaseInsensitive(request->current->path)) != db->usr_to_file.end()) {
       assert(!request->load_previous);
       request->load_previous = true;
       queue->load_previous_index.Enqueue(std::move(*request));
@@ -1299,6 +1340,7 @@ bool QueryDb_ImportMain(Config* config, QueryDatabase* db, ImportManager* import
 bool QueryDbMainLoop(
     Config* config,
     QueryDatabase* db,
+    bool* exit_when_idle,
     MultiQueueWaiter* waiter,
     QueueManager* queue,
     Project* project,
@@ -1336,14 +1378,15 @@ bool QueryDbMainLoop(
             << " with uri " << request->params.rootUri->raw_uri;
 
           if (!request->params.initializationOptions) {
-            LOG_S(INFO) << "Initialization parameters (particularily cacheDirectory) are required";
+            LOG_S(FATAL) << "Initialization parameters (particularily cacheDirectory) are required";
             exit(1);
           }
 
           *config = *request->params.initializationOptions;
 
           // Check client version.
-          if (config->clientVersion != kExpectedClientVersion) {
+          if (config->clientVersion != kExpectedClientVersion &&
+              config->clientVersion != -1 /*disable check*/) {
             Out_ShowLogMessage out;
             out.display_type = Out_ShowLogMessage::DisplayType::Show;
             out.params.type = lsMessageType::Error;
@@ -1375,8 +1418,8 @@ bool QueryDbMainLoop(
           }
           std::cerr << "[querydb] Starting " << config->indexerCount << " indexers" << std::endl;
           for (int i = 0; i < config->indexerCount; ++i) {
-            new std::thread([&]() {
-              IndexMain(config, file_consumer_shared, import_manager, timestamp_manager, project, working_files, waiter, queue);
+            WorkThread::StartThread("indexer" + std::to_string(i), [&]() {
+              return IndexMain(config, file_consumer_shared, import_manager, timestamp_manager, project, working_files, waiter, queue);
             });
           }
 
@@ -1395,7 +1438,7 @@ bool QueryDbMainLoop(
             //  << "] Dispatching index request for file " << entry.filename
             //  << std::endl;
             bool is_interactive = working_files->GetFileByFilename(entry.filename) != nullptr;
-            queue->index_request.Enqueue(Index_Request(entry.filename, entry.args, is_interactive));
+            queue->index_request.Enqueue(Index_Request(entry.filename, entry.args, is_interactive, nullopt));
           });
 
           // We need to support multiple concurrent index processes.
@@ -1459,7 +1502,7 @@ bool QueryDbMainLoop(
           LOG_S(INFO) << "[" << i << "/" << (project->entries.size() - 1)
             << "] Dispatching index request for file " << entry.filename;
           bool is_interactive = working_files->GetFileByFilename(entry.filename) != nullptr;
-          queue->index_request.Enqueue(Index_Request(entry.filename, entry.args, is_interactive));
+          queue->index_request.Enqueue(Index_Request(entry.filename, entry.args, is_interactive, nullopt));
         });
         break;
       }
@@ -1674,7 +1717,7 @@ bool QueryDbMainLoop(
 
         // Submit new index request.
         const Project::Entry& entry = project->FindCompilationEntryForFile(path);
-        queue->index_request.PriorityEnqueue(Index_Request(entry.filename, entry.args, true /*is_interactive*/));
+        queue->index_request.PriorityEnqueue(Index_Request(entry.filename, entry.args, true /*is_interactive*/, nullopt));
 
         break;
       }
@@ -1719,7 +1762,7 @@ bool QueryDbMainLoop(
         //      if so, ignore that index response.
         // TODO: send as priority request
         Project::Entry entry = project->FindCompilationEntryForFile(path);
-        queue->index_request.Enqueue(Index_Request(entry.filename, entry.args, true /*is_interactive*/));
+        queue->index_request.Enqueue(Index_Request(entry.filename, entry.args, true /*is_interactive*/, nullopt));
 
         clang_complete->NotifySave(path);
 
@@ -2572,6 +2615,45 @@ bool QueryDbMainLoop(
         break;
       }
 
+      case IpcId::CqueryIndexFile: {
+        auto msg = static_cast<Ipc_CqueryIndexFile*>(message.get());
+        queue->index_request.Enqueue(Index_Request(
+            NormalizePath(msg->params.path),
+            msg->params.args,
+            msg->params.is_interactive,
+            msg->params.contents));
+        break;
+      }
+
+      case IpcId::CqueryQueryDbWaitForIdleIndexer: {
+        auto msg = static_cast<Ipc_CqueryQueryDbWaitForIdleIndexer*>(message.get());
+        LOG_S(INFO) << "Waiting for idle";
+        int idle_count = 0;
+        while (true) {
+          bool has_work = false;
+          has_work |= import_manager->HasActiveImports();
+          has_work |= queue->HasWork();
+          has_work |= QueryDb_ImportMain(config, db, import_manager, queue, working_files);
+          if (!has_work)
+            ++idle_count;
+          else
+            idle_count = 0;
+
+          // There are race conditions between each of the three checks above,
+          // so we retry a bunch of times to try to avoid any.
+          if (idle_count > 10)
+            break;
+        }
+        LOG_S(INFO) << "Done waiting for idle";
+        break;
+      }
+
+      case IpcId::CqueryExitWhenIdle: {
+        *exit_when_idle = true;
+        WorkThread::request_exit_on_idle = true;
+        break;
+      }
+
       default: {
         LOG_S(INFO) << "[querydb] Unhandled IPC message " << IpcIdToString(message->method_id);
         exit(1);
@@ -2588,10 +2670,8 @@ bool QueryDbMainLoop(
   return did_work;
 }
 
-void QueryDbMain(const std::string& bin_name, Config* config, MultiQueueWaiter* waiter) {
-  // Create queues.
-  QueueManager queue(waiter);
-
+void RunQueryDbThread(const std::string& bin_name, Config* config, MultiQueueWaiter* waiter, QueueManager* queue) {
+  bool exit_when_idle = false;
   Project project;
   WorkingFiles working_files;
   ClangCompleteManager clang_complete(
@@ -2610,18 +2690,22 @@ void QueryDbMain(const std::string& bin_name, Config* config, MultiQueueWaiter*
   QueryDatabase db;
   while (true) {
     bool did_work = QueryDbMainLoop(
-      config, &db, waiter, &queue,
+      config, &db, &exit_when_idle, waiter, queue,
       &project, &file_consumer_shared, &import_manager, &timestamp_manager, &working_files,
       &clang_complete, &include_complete, global_code_complete_cache.get(), non_global_code_complete_cache.get(), signature_cache.get());
 
+    // No more work left and exit request. Exit.
+    if (!did_work && exit_when_idle && WorkThread::num_active_threads == 0)
+      exit(0);
+
     // Cleanup and free any unused memory.
     FreeUnusedMemory();
 
     if (!did_work) {
       waiter->Wait({
         IpcManager::instance()->threaded_queue_for_server_.get(),
-        &queue.do_id_map,
-        &queue.on_indexed
+        &queue->do_id_map,
+        &queue->on_indexed
       });
     }
   }
@@ -2688,8 +2772,6 @@ void QueryDbMain(const std::string& bin_name, Config* config, MultiQueueWaiter*
 
 
 
-
-// TODO: global lock on stderr output.
 
 // Separate thread whose only job is to read from stdin and
 // dispatch read commands to the actual indexer program. This
@@ -2697,16 +2779,16 @@ void QueryDbMain(const std::string& bin_name, Config* config, MultiQueueWaiter*
 // blocks.
 //
 // |ipc| is connected to a server.
-void LanguageServerStdinLoop(Config* config, std::unordered_map<IpcId, Timer>* request_times) {
-  IpcManager* ipc = IpcManager::instance();
+void LaunchStdinLoop(Config* config, std::unordered_map<IpcId, Timer>* request_times) {
+
+  WorkThread::StartThread("stdin", [config, request_times]() {
+    IpcManager* ipc = IpcManager::instance();
 
-  SetCurrentThreadName("stdin");
-  while (true) {
     std::unique_ptr<BaseIpcMessage> message = MessageRegistry::instance()->ReadMessageFromStdin();
 
     // Message parsing can fail if we don't recognize the method.
     if (!message)
-      continue;
+      return WorkThread::Result::MoreWork;
 
     (*request_times)[message->method_id] = Timer();
 
@@ -2722,8 +2804,21 @@ void LanguageServerStdinLoop(Config* config, std::unordered_map<IpcId, Timer>* r
       break;
     }
 
+    case IpcId::Exit: {
+      exit(0);
+      break;
+    }
+
+    case IpcId::CqueryExitWhenIdle: {
+      // querydb needs to know to exit when idle. We return out of the stdin
+      // loop to exit the thread. If we keep parsing input stdin is likely
+      // closed so cquery will exit.
+      LOG_S(INFO) << "cquery will exit when all threads are idle";
+      ipc->SendMessage(IpcManager::Destination::Server, std::move(message));
+      return WorkThread::Result::ExitThread;
+    }
+
     case IpcId::Initialize:
-    case IpcId::Exit:
     case IpcId::TextDocumentDidOpen:
     case IpcId::TextDocumentDidChange:
     case IpcId::TextDocumentDidClose:
@@ -2747,7 +2842,9 @@ void LanguageServerStdinLoop(Config* config, std::unordered_map<IpcId, Timer>* r
     case IpcId::CqueryVars:
     case IpcId::CqueryCallers:
     case IpcId::CqueryBase:
-    case IpcId::CqueryDerived: {
+    case IpcId::CqueryDerived:
+    case IpcId::CqueryIndexFile:
+    case IpcId::CqueryQueryDbWaitForIdleIndexer: {
       ipc->SendMessage(IpcManager::Destination::Server, std::move(message));
       break;
     }
@@ -2757,7 +2854,9 @@ void LanguageServerStdinLoop(Config* config, std::unordered_map<IpcId, Timer>* r
       exit(1);
     }
     }
-  }
+
+    return WorkThread::Result::MoreWork;
+  });
 }
 
 
@@ -2805,15 +2904,14 @@ void LanguageServerStdinLoop(Config* config, std::unordered_map<IpcId, Timer>* r
 
 
 
-void StdoutMain(std::unordered_map<IpcId, Timer>* request_times, MultiQueueWaiter* waiter) {
-  SetCurrentThreadName("stdout");
-  IpcManager* ipc = IpcManager::instance();
+void LaunchStdoutThread(std::unordered_map<IpcId, Timer>* request_times, MultiQueueWaiter* waiter, QueueManager* queue) {
+  WorkThread::StartThread("stdout", [=]() {
+    IpcManager* ipc = IpcManager::instance();
 
-  while (true) {
     std::vector<std::unique_ptr<BaseIpcMessage>> messages = ipc->GetMessages(IpcManager::Destination::Client);
     if (messages.empty()) {
-      waiter->Wait({ipc->threaded_queue_for_client_.get()});
-      continue;
+      waiter->Wait({ ipc->threaded_queue_for_client_.get() });
+      return queue->HasWork() ? WorkThread::Result::MoreWork : WorkThread::Result::NoWork;
     }
 
     for (auto& message : messages) {
@@ -2839,26 +2937,24 @@ void StdoutMain(std::unordered_map<IpcId, Timer>* request_times, MultiQueueWaite
         }
       }
     }
-  }
+
+    return WorkThread::Result::MoreWork;
+  });
 }
 
 void LanguageServerMain(const std::string& bin_name, Config* config, MultiQueueWaiter* waiter) {
+  QueueManager queue(waiter);
   std::unordered_map<IpcId, Timer> request_times;
 
-  // Start stdin reader. Reading from stdin is a blocking operation so this
-  // needs a dedicated thread.
-  new std::thread([&]() {
-    LanguageServerStdinLoop(config, &request_times);
-  });
-
-  // Start querydb thread. querydb will start indexer threads as needed.
-  new std::thread([&]() {
-    QueryDbMain(bin_name, config, waiter);
-  });
+  LaunchStdinLoop(config, &request_times);
 
   // We run a dedicated thread for writing to stdout because there can be an
   // unknown number of delays when output information.
-  StdoutMain(&request_times, waiter);
+  LaunchStdoutThread(&request_times, waiter, &queue);
+
+  // Start querydb which takes over this thread. The querydb will launch
+  // indexer threads as needed.
+  RunQueryDbThread(bin_name, config, waiter, &queue);
 }
 
 
diff --git a/src/include_complete.cc b/src/include_complete.cc
index cf120747..e3362d43 100644
--- a/src/include_complete.cc
+++ b/src/include_complete.cc
@@ -5,6 +5,7 @@
 #include "project.h"
 #include "standard_includes.h"
 #include "timer.h"
+#include "work_thread.h"
 
 #include <thread>
 
@@ -114,8 +115,7 @@ void IncludeComplete::Rescan() {
     match_ = MakeUnique<GroupMatch>(config_->includeCompletionWhitelist, config_->includeCompletionBlacklist);
 
   is_scanning = true;
-  new std::thread([this]() {
-    SetCurrentThreadName("include_scanner");
+  WorkThread::StartThread("include_scanner", [this]() {
     Timer timer;
 
     InsertStlIncludes();
@@ -127,6 +127,8 @@ void IncludeComplete::Rescan() {
 
     timer.ResetAndPrint("[perf] Scanning for includes");
     is_scanning = false;
+
+    return WorkThread::Result::ExitThread;
   });
 }
 
diff --git a/src/ipc.cc b/src/ipc.cc
index ba03cc1c..60db889a 100644
--- a/src/ipc.cc
+++ b/src/ipc.cc
@@ -71,6 +71,14 @@ const char* IpcIdToString(IpcId id) {
 
   case IpcId::Cout:
     return "$cout";
+
+  case IpcId::CqueryIndexFile:
+    return "$cquery/indexFile";
+  case IpcId::CqueryQueryDbWaitForIdleIndexer:
+    return "$cquery/queryDbWaitForIdleIndexer";
+  case IpcId::CqueryExitWhenIdle:
+    return "$cquery/exitWhenIdle";
+
   default:
     assert(false && "missing IpcId string name");
     exit(1);
diff --git a/src/ipc.h b/src/ipc.h
index 2a89ee7d..a0811fd3 100644
--- a/src/ipc.h
+++ b/src/ipc.h
@@ -46,7 +46,14 @@ enum class IpcId : int {
   CqueryDerived,    // Show all derived types/methods.
 
   // Internal implementation detail.
-  Cout
+  Cout,
+
+  // Index the given file contents. Used in tests.
+  CqueryIndexFile,
+  // Make querydb wait for the indexer to be idle. Used in tests.
+  CqueryQueryDbWaitForIdleIndexer,
+  // Exit after all messages have been read/processes. Used in tests.
+  CqueryExitWhenIdle
 };
 MAKE_ENUM_HASHABLE(IpcId)
 MAKE_REFLECT_TYPE_PROXY(IpcId, int)
@@ -68,4 +75,28 @@ struct Ipc_Cout : public IpcMessage<Ipc_Cout> {
   std::string content;
   IpcId original_ipc_id;
 };
-MAKE_REFLECT_STRUCT(Ipc_Cout, content);
\ No newline at end of file
+MAKE_REFLECT_STRUCT(Ipc_Cout, content);
+
+struct Ipc_CqueryIndexFile : public IpcMessage<Ipc_CqueryIndexFile> {
+  static constexpr IpcId kIpcId = IpcId::CqueryIndexFile;
+
+  struct Params {
+    std::string path;
+    std::vector<std::string> args;
+    bool is_interactive = false;
+    std::string contents;
+  };
+  Params params;
+};
+MAKE_REFLECT_STRUCT(Ipc_CqueryIndexFile::Params, path, args, is_interactive, contents);
+MAKE_REFLECT_STRUCT(Ipc_CqueryIndexFile, params);
+
+struct Ipc_CqueryQueryDbWaitForIdleIndexer : public IpcMessage<Ipc_CqueryQueryDbWaitForIdleIndexer> {
+  static constexpr IpcId kIpcId = IpcId::CqueryQueryDbWaitForIdleIndexer;
+};
+MAKE_REFLECT_EMPTY_STRUCT(Ipc_CqueryQueryDbWaitForIdleIndexer);
+
+struct Ipc_CqueryExitWhenIdle : public IpcMessage<Ipc_CqueryExitWhenIdle> {
+  static constexpr IpcId kIpcId = IpcId::CqueryExitWhenIdle;
+};
+MAKE_REFLECT_EMPTY_STRUCT(Ipc_CqueryExitWhenIdle);
\ No newline at end of file
diff --git a/src/language_server_api.cc b/src/language_server_api.cc
index 08d3c062..9fa9dd7c 100644
--- a/src/language_server_api.cc
+++ b/src/language_server_api.cc
@@ -1,5 +1,8 @@
 #include "language_server_api.h"
 
+#include <doctest/doctest.h>
+#include <loguru.hpp>
+
 void Reflect(Writer& visitor, lsRequestId& value) {
   assert(value.id0.has_value() || value.id1.has_value());
 
@@ -22,55 +25,113 @@ void Reflect(Reader& visitor, lsRequestId& id) {
 
 MessageRegistry* MessageRegistry::instance_ = nullptr;
 
-std::unique_ptr<BaseIpcMessage> MessageRegistry::ReadMessageFromStdin() {
-  int content_length = -1;
-  int iteration = 0;
+// Reads a JsonRpc message. |read| returns the next input character.
+optional<std::string> ReadJsonRpcContentFrom(std::function<optional<char>()> read) {
+  // Read the content length. It is terminated by the "\r\n" sequence.
+  int exit_seq = 0;
+  std::string stringified_content_length;
   while (true) {
-    if (++iteration > 10) {
-      assert(false && "bad parser state");
-      exit(1);
+    optional<char> opt_c = read();
+    if (!opt_c) {
+      LOG_S(INFO) << "No more input when reading content length header";
+      return nullopt;
     }
+    char c = *opt_c;
 
-    std::string line;
-    std::getline(std::cin, line);
+    if (exit_seq == 0 && c == '\r') ++exit_seq;
+    if (exit_seq == 1 && c == '\n') break;
+    
+    stringified_content_length += c;
+  }
+  constexpr char* kContentLengthStart = "Content-Length: ";
+  assert(StartsWith(stringified_content_length, kContentLengthStart));
+  int content_length = atoi(stringified_content_length.c_str() + strlen(kContentLengthStart));
 
-    // No content; end of stdin.
-    if (line.empty()) {
-      std::cerr << "stdin closed; exiting" << std::endl;
-      exit(0);
-    }
-
-    // std::cin >> line;
-    // std::cerr << "Read line " << line;
-
-    if (line.compare(0, 14, "Content-Length") == 0) {
-      content_length = atoi(line.c_str() + 16);
-    }
-
-    if (line == "\r")
-      break;
+  // There is always a "\r\n" sequence before the actual content.
+  auto expect_char = [&](char expected) {
+    optional<char> opt_c = read();
+    return opt_c && *opt_c == expected;
+  };
+  if (!expect_char('\r') || !expect_char('\n')) {
+    LOG_S(INFO) << "Unexpected token (expected \r\n sequence)";
+    return nullopt;
   }
 
-  // bad input that is not a message.
-  if (content_length < 0) {
-    std::cerr << "parsing command failed (no Content-Length header)"
-      << std::endl;
-    return nullptr;
-  }
-
-  // TODO: maybe use std::cin.read(c, content_length)
+  // Read content.
   std::string content;
   content.reserve(content_length);
-  for (int i = 0; i < content_length; ++i) {
-    char c;
-    std::cin.read(&c, 1);
-    content += c;
+  for (size_t i = 0; i < content_length; ++i) {
+    optional<char> c = read();
+    if (!c) {
+      LOG_S(INFO) << "No more input when reading content body";
+      return nullopt;
+    }
+    content += *c;
+  }
+  
+  return content;
+}
+
+TEST_SUITE("FindIncludeLine");
+
+auto MakeContentReader(std::string* content, bool can_be_empty) {
+  return [=]() -> optional<char> {
+    if (!can_be_empty)
+      REQUIRE(!content->empty());
+    if (content->empty())
+      return nullopt;
+    char c = (*content)[0];
+    content->erase(content->begin());
+    return c;
+  };
+}
+
+TEST_CASE("ReadContentFromSource") {
+  auto parse_correct = [](std::string content) {
+    auto reader = MakeContentReader(&content, false /*can_be_empty*/);
+    auto got = ReadJsonRpcContentFrom(reader);
+    REQUIRE(got);
+    return got.value();
+  };
+
+  auto parse_incorrect = [](std::string content) {
+    auto reader = MakeContentReader(&content, true /*can_be_empty*/);
+    return ReadJsonRpcContentFrom(reader);
+  };
+
+  REQUIRE(parse_correct("Content-Length: 0\r\n\r\n") == "");
+  REQUIRE(parse_correct("Content-Length: 1\r\n\r\na") == "a");
+  REQUIRE(parse_correct("Content-Length: 4\r\n\r\nabcd") == "abcd");
+
+  REQUIRE(parse_incorrect("ggg") == optional<std::string>());
+  REQUIRE(parse_incorrect("Content-Length: 0\r\n") == optional<std::string>());
+  REQUIRE(parse_incorrect("Content-Length: 5\r\n\r\nab") == optional<std::string>());
+}
+
+TEST_SUITE_END();
+
+optional<char> ReadCharFromStdinBlocking() {
+  // Bad stdin means parent process has probably exited. Either way, cquery
+  // can no longer be communicated with so just exit.
+  if (!std::cin.good()) {
+    LOG_S(FATAL) << "std::cin.good() is false; exiting";
+    exit(1);
   }
 
-  //std::cerr << content.c_str() << std::endl;
+  char c = 0;
+  std::cin.read(&c, 1);
+  return c;
+}
+
+std::unique_ptr<BaseIpcMessage> MessageRegistry::ReadMessageFromStdin() {
+  optional<std::string> content = ReadJsonRpcContentFrom(&ReadCharFromStdinBlocking);
+  if (!content) {
+    LOG_S(FATAL) << "Failed to read JsonRpc input; exiting";
+    exit(1);
+  }
 
   rapidjson::Document document;
-  document.Parse(content.c_str(), content_length);
+  document.Parse(content->c_str(), content->length());
   assert(!document.HasParseError());
 
   return Parse(document);
@@ -86,7 +147,7 @@ std::unique_ptr<BaseIpcMessage> MessageRegistry::Parse(Reader& visitor) {
   ReflectMember(visitor, "method", method);
 
   if (allocators.find(method) == allocators.end()) {
-    std::cerr << "Unable to find registered handler for method \"" << method << "\"" << std::endl;
+    LOG_S(ERROR) << "Unable to find registered handler for method \"" << method << "\"" << std::endl;
     return nullptr;
   }
 
diff --git a/src/threaded_queue.h b/src/threaded_queue.h
index 93f7a1e3..8df109f7 100644
--- a/src/threaded_queue.h
+++ b/src/threaded_queue.h
@@ -1,5 +1,6 @@
 #pragma once
 
+#include "work_thread.h"
 #include <optional.h>
 
 #include <algorithm>
@@ -38,8 +39,11 @@ struct MultiQueueWaiter {
     // HasState() is called data gets posted but before we begin waiting for
     // the condition variable, we will miss the notification. The timeout of 5
     // means that if this happens we will delay operation for 5 seconds.
+    //
+    // If we're trying to exit (WorkThread::request_exit_on_idle), do not
+    // bother waiting.
 
-    while (!HasState(queues)) {
+    while (!HasState(queues) && !WorkThread::request_exit_on_idle) {
       std::unique_lock<std::mutex> l(m);
       cv.wait_for(l, std::chrono::seconds(5));
     }
@@ -132,7 +136,8 @@ public:
 
   // Get the first element from the queue without blocking. Returns a null
   // value if the queue is empty.
-  optional<T> TryDequeue() {
+  template<typename TAction>
+  optional<T> TryDequeuePlusAction(TAction action) {
     std::lock_guard<std::mutex> lock(mutex_);
     if (priority_.empty() && queue_.empty())
       return nullopt;
@@ -145,9 +150,16 @@ public:
 
     auto val = std::move(queue_.front());
     queue_.pop();
+
+    action(val);
+
     return std::move(val);
   }
 
+  optional<T> TryDequeue() {
+    return TryDequeuePlusAction([](const T&) {});
+  }
+
  private:
   std::queue<T> priority_;
   mutable std::mutex mutex_;
diff --git a/src/work_thread.cc b/src/work_thread.cc
new file mode 100644
index 00000000..f6b905b4
--- /dev/null
+++ b/src/work_thread.cc
@@ -0,0 +1,28 @@
+#include "work_thread.h"
+
+#include "platform.h"
+
+std::atomic<int> WorkThread::num_active_threads;
+std::atomic<bool> WorkThread::request_exit_on_idle;
+
+// static
+void WorkThread::StartThread(
+    const std::string& thread_name,
+    const std::function<Result()>& entry_point) {
+  new std::thread([thread_name, entry_point]() {
+    SetCurrentThreadName(thread_name);
+
+    ++num_active_threads;
+
+    // Main loop.
+    while (true) {
+      Result result = entry_point();
+      if (result == Result::ExitThread)
+        break;
+      if (request_exit_on_idle && result == Result::NoWork)
+        break;
+    }
+
+    --num_active_threads;
+  });
+}
\ No newline at end of file
diff --git a/src/work_thread.h b/src/work_thread.h
new file mode 100644
index 00000000..6a80c547
--- /dev/null
+++ b/src/work_thread.h
@@ -0,0 +1,31 @@
+#pragma once
+
+#include <atomic>
+#include <functional>
+#include <mutex>
+#include <thread>
+#include <vector>
+
+// Helper methods for starting threads that do some work. Enables test code to
+// wait for all work to complete.
+struct WorkThread {
+  enum class Result {
+    MoreWork,
+    NoWork,
+    ExitThread
+  };
+
+  // The number of active worker threads.
+  static std::atomic<int> num_active_threads;
+  // Set to true to request all work thread instances to exit.
+  static std::atomic<bool> request_exit_on_idle;
+
+  // Launch a new thread. |entry_point| will be called continously. It should
+  // return true if it there is still known work to be done.
+  static void StartThread(
+      const std::string& thread_name,
+      const std::function<Result()>& entry_point);
+
+  // Static-only class.
+  WorkThread() = delete;
+};
\ No newline at end of file
diff --git a/test_runner_e2e.py b/test_runner_e2e.py
index b1c350d0..617a3397 100644
--- a/test_runner_e2e.py
+++ b/test_runner_e2e.py
@@ -1,7 +1,12 @@
 import json
+import re
 import shlex
 from subprocess import Popen, PIPE
 
+
+CQUERY_PATH = 'x64/Debug/cquery.exe'
+CACHE_DIR = 'e2e_CACHE'
+
     # Content-Length: ...\r\n
     # \r\n
     # {
@@ -22,15 +27,33 @@ from subprocess import Popen, PIPE
 
 class TestBuilder:
   def __init__(self):
-    self.files = []
     self.sent = []
-    self.received = []
+    self.expected = []
 
-  def WithFile(self, filename, contents):
+  def IndexFile(self, path, contents):
     """
     Writes the file contents to disk so that the language server can access it.
     """
-    self.files.append((filename, contents))
+    self.Send({
+      'method': '$cquery/indexFile',
+      'params': {
+        'path': path,
+        'contents': contents,
+        'args': [
+          '-xc++',
+          '-std=c++11',
+          '-isystemC:/Program Files (x86)/Microsoft Visual Studio/2017/Community/VC/Tools/MSVC/14.10.25017/include',
+          '-isystemC:/Program Files (x86)/Windows Kits/10/Include/10.0.15063.0/ucrt'
+        ]
+      }
+    })
+    return self
+
+  def WaitForIdle(self):
+    """
+    Blocks the querydb thread until any active imports are complete.
+    """
+    self.Send({'method': '$cquery/queryDbWaitForIdleIndexer'})
     return self
 
   def Send(self, stdin):
@@ -41,11 +64,12 @@ class TestBuilder:
     self.sent.append(stdin)
     return self
 
-  def Expect(self, stdout):
+  def Expect(self, expected):
     """
     Expect a message from the language server.
     """
-    self.received.append(stdout)
+    expected['jsonrpc'] = '2.0'
+    self.expected.append(expected)
     return self
 
   def SetupCommonInit(self):
@@ -57,15 +81,45 @@ class TestBuilder:
       'method': 'initialize',
       'params': {
         'processId': 123,
-        'rootPath': 'cquery',
+        'rootUri': 'cquery',
         'capabilities': {},
-        'trace': 'off'
+        'trace': 'off',
+        'initializationOptions': {
+          'cacheDirectory': CACHE_DIR,
+          'clientVersion': -1 # Disables the check
+        }
       }
     })
     self.Expect({
       'id': 0,
-      'method': 'initialized',
-      'result': {}
+      'result': {
+        'capabilities': {
+          'textDocumentSync': 2,
+          'hoverProvider': True,
+          'completionProvider': {
+            'resolveProvider': False,
+            'triggerCharacters': [ '.', ':', '>', '#' ]
+          },
+          'signatureHelpProvider': {
+            'triggerCharacters': [ '(', ',' ]
+          },
+          'definitionProvider': True,
+          'referencesProvider': True,
+          'documentHighlightProvider': True,
+          'documentSymbolProvider': True,
+          'workspaceSymbolProvider': True,
+          'codeActionProvider': True,
+          'codeLensProvider': {
+            'resolveProvider': False
+          },
+          'documentFormattingProvider': False,
+          'documentRangeFormattingProvider': False,
+          'renameProvider': True,
+          'documentLinkProvider': {
+            'resolveProvider': False
+          }
+        }
+      }
     })
     return self
 
@@ -79,32 +133,76 @@ def _ExecuteTest(name, func):
   if not isinstance(test_builder, TestBuilder):
     raise Exception('%s does not return a TestBuilder instance' % name)
 
-  test_builder.Send({ 'method': 'exit' })
-
-  # Possible test runner implementation
-  cmd = "x64/Debug/indexer.exe --language-server"
-  process = Popen(shlex.split(cmd), stdin=PIPE, stdout=PIPE, stderr=PIPE, universal_newlines=True)
+  # Add a final exit message.
+  test_builder.Send({ 'method': '$cquery/exitWhenIdle' })
 
+  # Convert messages to a stdin byte array.
   stdin = ''
   for message in test_builder.sent:
     payload = json.dumps(message)
     wrapped = 'Content-Length: %s\r\n\r\n%s' % (len(payload), payload)
     stdin += wrapped
+  stdin_bytes = stdin.encode(encoding='UTF-8')
 
-  print('## %s ##' % name)
-  print('== STDIN ==')
-  print(stdin)
-  (stdout, stderr) = process.communicate(stdin)
-  if stdout:
-    print('== STDOUT ==')
-    print(stdout)
-  if stderr:
-    print('== STDERR ==')
-    print(stderr)
+  # Finds all messages in |string| by parsing Content-Length headers.
+  def GetMessages(string):
+    messages = []
+    for match in re.finditer('Content-Length: (\d+)\r\n\r\n', string):
+      start = match.span()[1]
+      length = int(match.groups()[0])
+      message = string[start:start + length]
+      messages.append(json.loads(message))
+    return messages
 
-  # TODO: Actually verify stdout.
+  # Utility method to print a byte array.
+  def PrintByteArray(bytes):
+    for line in bytes.split(b'\r\n'):
+      print(line.decode('utf8'))
+
+  # Execute program.
+  cmd = "%s --language-server" % CQUERY_PATH
+  process = Popen(shlex.split(cmd), stdin=PIPE, stdout=PIPE, stderr=PIPE)
+  (stdout, stderr) = process.communicate(stdin_bytes)
+  exit_code = process.wait();
+
+  # Check if test succeeded.
+  actual = GetMessages(stdout.decode('utf8'))
+  success = actual == test_builder.expected
+
+  # Print failure messages.
+  if success:
+    print('== Passed %s with exit_code=%s ==' % (name, exit_code))
+  else:
+    print('== FAILED %s with exit_code=%s ==' % (name, exit_code))
+    print('## STDIN:')
+    for message in GetMessages(stdin):
+      print(json.dumps(message, indent=True))
+    if stdout:
+      print('## STDOUT:')
+      for message in GetMessages(stdout.decode('utf8')):
+        print(json.dumps(message, indent=True))
+    if stderr:
+      print('## STDERR:')
+      PrintByteArray(stderr)
+
+    print('## Expected output')
+    for message in test_builder.expected:
+      print(message)
+    print('## Actual output')
+    for message in actual:
+      print(message)
+    print('## Difference')
+    common_end = min(len(test_builder.expected), len(actual))
+    for i in range(0, common_end):
+      if test_builder.expected[i] != actual[i]:
+        print('i=%s' % i)
+        print('- Expected %s' % str(test_builder.expected[i]))
+        print('- Actual %s' % str(actual[i]))
+    for i in range(common_end, len(test_builder.expected)):
+      print('Extra expected: %s' % str(test_builder.expected[i]))
+    for i in range(common_end, len(actual)):
+      print('Extra actual: %s' % str(actual[i]))
 
-  exit_code = process.wait()
 
 def _DiscoverTests():
   """
@@ -122,12 +220,16 @@ def _RunTests():
   Executes all tests.
   """
   for name, func in _DiscoverTests():
-    print('Running test function %s' % name)
     _ExecuteTest(name, func)
 
 
 
 
+
+
+#### EXAMPLE TESTS ####
+
+
 class lsSymbolKind:
   Function = 1
 
@@ -138,24 +240,32 @@ def lsSymbolInfo(name, position, kind):
     'kind': kind
   }
 
-def Test_Init():
+def DISABLED_Test_Init():
   return (TestBuilder()
     .SetupCommonInit()
   )
 
-def _Test_Outline():
+def Test_Outline():
   return (TestBuilder()
     .SetupCommonInit()
-    .WithFile("foo.cc",
-      """
-      void main() {}
-      """
-    )
+    # .IndexFile("file:///C%3A/Users/jacob/Desktop/cquery/foo.cc",
+    .IndexFile("foo.cc",
+      """void foobar();""")
+    .WaitForIdle()
     .Send({
       'id': 1,
       'method': 'textDocument/documentSymbol',
-      'params': {}
+      'params': {
+        'textDocument': {
+          'uri': 'C:/Users/jacob/Desktop/cquery/foo.cc'
+        }
+      }
     })
+    # .Expect({
+    #   'jsonrpc': '2.0',
+    #   'id': 1,
+    #   'error': {'code': -32603, 'message': 'Unable to find file '}
+    # }))
     .Expect({
       'id': 1,
       'result': [
@@ -165,4 +275,4 @@ def _Test_Outline():
 
 
 if __name__ == '__main__':
-  _RunTests()
\ No newline at end of file
+  _RunTests()