diff --git a/src/command_line.cc b/src/command_line.cc
index ab6c45c1..a53aca57 100644
--- a/src/command_line.cc
+++ b/src/command_line.cc
@@ -480,6 +480,8 @@ Command line options:
   --language-server
                 Run as a language server. This implements the language server
                 spec over STDIN and STDOUT.
+  --init <initializationOptions>
+                Override user provided initialization options.
   --test-unit   Run unit tests.
   --test-index <opt_filter_path>
                 Run index tests. opt_filter_path can be used to specify which
diff --git a/src/indexer.cc b/src/indexer.cc
index 81894292..32332e1d 100644
--- a/src/indexer.cc
+++ b/src/indexer.cc
@@ -12,6 +12,7 @@
 #include <algorithm>
 #include <chrono>
 #include <climits>
+#include <iostream>
 
 // TODO: See if we can use clang_indexLoc_getFileLocation to get a type ref on
 // |Foobar| in DISALLOW_COPY(Foobar)
diff --git a/src/indexer.h b/src/indexer.h
index 13547e16..d5fea6f7 100644
--- a/src/indexer.h
+++ b/src/indexer.h
@@ -19,8 +19,6 @@
 #include <algorithm>
 #include <cassert>
 #include <cstdint>
-#include <fstream>
-#include <iostream>
 #include <unordered_map>
 #include <vector>
 
diff --git a/src/messages/cquery_call_tree.cc b/src/messages/cquery_call_tree.cc
index 3b3dfbb1..679982f0 100644
--- a/src/messages/cquery_call_tree.cc
+++ b/src/messages/cquery_call_tree.cc
@@ -2,6 +2,8 @@
 #include "query_utils.h"
 #include "queue_manager.h"
 
+#include <loguru.hpp>
+
 namespace {
 struct Ipc_CqueryCallTreeInitial
     : public IpcMessage<Ipc_CqueryCallTreeInitial> {
@@ -100,7 +102,7 @@ std::vector<Out_CqueryCallTree::CallEntry> BuildExpandCallTree(
     // TODO: REMOVE |seen_locations| once we fix the querydb update bugs
     // TODO: basically, querydb gets duplicate references inserted into it.
     if (!seen_locations.insert(caller.loc).second) {
-      std::cerr << "!!!! FIXME DUPLICATE REFERENCE IN QUERYDB" << std::endl;
+      LOG_S(ERROR) << "!!!! FIXME DUPLICATE REFERENCE IN QUERYDB" << std::endl;
       return;
     }
 
diff --git a/src/messages/initialize.cc b/src/messages/initialize.cc
index 95c5e1e1..f0ff3d4b 100644
--- a/src/messages/initialize.cc
+++ b/src/messages/initialize.cc
@@ -10,6 +10,8 @@
 
 #include <loguru.hpp>
 
+#include <iostream>
+
 // TODO Cleanup global variables
 extern std::string g_init_options;
 extern int g_enable_comments;