diff --git a/src/lib/Application.cpp b/src/lib/Application.cpp
index 1eafe428..464923e3 100644
--- a/src/lib/Application.cpp
+++ b/src/lib/Application.cpp
@@ -1,14 +1,11 @@
 #include "Application.h"
 
-#include "utility/file/FileSystem.h"
 #include "utility/logging/ConsoleLogger.h"
 #include "utility/logging/FileLogger.h"
 #include "utility/logging/logging.h"
 #include "utility/logging/LogManager.h"
 #include "utility/messaging/MessageQueue.h"
-#include "utility/messaging/type/MessageActivateNodes.h"
 #include "utility/messaging/type/MessageDispatchWhenLicenseValid.h"
-#include "utility/messaging/type/MessageScrollSpeedChange.h"
 #include "utility/messaging/type/MessageStatus.h"
 #include "utility/messaging/type/MessageShowStartScreen.h"
 #include "utility/scheduling/TaskScheduler.h"
@@ -26,7 +23,6 @@
 #include "LicenseChecker.h"
 #include "settings/ApplicationSettings.h"
 #include "settings/ColorScheme.h"
-#include "settings/ProjectSettings.h"
 
 void Application::createInstance(
 	const Version& version, ViewFactory* viewFactory, NetworkFactory* networkFactory
@@ -57,7 +53,8 @@ void Application::createInstance(
 
 	if (networkFactory != nullptr)
 	{
-		s_instance->m_ideCommunicationController = networkFactory->createIDECommunicationController(s_instance->m_storageCache.get());
+		s_instance->m_ideCommunicationController =
+			networkFactory->createIDECommunicationController(s_instance->m_storageCache.get());
 	}
 
 	s_instance->startMessagingAndScheduling();
@@ -224,33 +221,18 @@ void Application::handleMessage(MessageLoadProject* message)
 		return;
 	}
 
-	if (message->forceRefresh && !isTrial())
+	if (m_project && projectSettingsFilePath == m_project->getProjectSettingsFilePath())
 	{
-		if (m_hasGUI)
+		if (message->forceRefresh)
 		{
-			std::vector<std::string> options;
-			options.push_back("Yes");
-			options.push_back("No");
-			int result = handleDialog(
-				"Some settings were changed, the project needs to be fully reindexed. "
-				"Do you want to reindex the project?", options);
-
-			if (result == 1)
-			{
-				if (!m_project || projectSettingsFilePath != m_project->getProjectSettingsFilePath())
-				{
-					createAndLoadProject(projectSettingsFilePath);
-					return;
-				}
-			}
+			m_project->setStateSettingsUpdated();
+			m_project->refresh(false);
 		}
 
-		refreshProject(true);
-	}
-	else if (!m_project || projectSettingsFilePath != m_project->getProjectSettingsFilePath())
-	{
-		createAndLoadProject(projectSettingsFilePath);
+		return;
 	}
+
+	createAndLoadProject(projectSettingsFilePath);
 }
 
 void Application::handleMessage(MessageRefresh* message)
diff --git a/src/lib/Project.cpp b/src/lib/Project.cpp
index 51b494fb..de628dab 100644
--- a/src/lib/Project.cpp
+++ b/src/lib/Project.cpp
@@ -2,7 +2,6 @@
 
 #include "component/view/DialogView.h"
 #include "data/access/StorageAccessProxy.h"
-#include "data/graph/Token.h"
 #include "data/parser/cxx/TaskParseWrapper.h"
 #include "data/parser/java/TaskParseJava.h"
 #include "data/PersistentStorage.h"
@@ -11,9 +10,8 @@
 #include "settings/ProjectSettings.h"
 
 #include "utility/file/FileRegister.h"
-#include "utility/file/FileSystem.h"
-#include "utility/logging/logging.h"
 #include "utility/messaging/type/MessageFinishedParsing.h"
+#include "utility/messaging/type/MessageRefresh.h"
 #include "utility/messaging/type/MessageStatus.h"
 #include "utility/scheduling/TaskGroupSequential.h"
 #include "utility/scheduling/TaskGroupParallel.h"
@@ -66,19 +64,81 @@ Project::~Project()
 
 bool Project::refresh(bool forceRefresh)
 {
-	if (allowsRefresh())
+	if (m_state == PROJECT_STATE_NOT_LOADED)
 	{
-		getProjectSettings()->reload();
+		return false;
+	}
 
-		updateFileManager(m_fileManager);
+	std::string question;
 
-		if (buildIndex(forceRefresh))
+	if (!forceRefresh)
+	{
+		switch (m_state)
 		{
-			m_state = PROJECT_STATE_LOADED;
-			return true;
+			case PROJECT_STATE_EMPTY:
+				forceRefresh = true;
+				break;
+
+			case PROJECT_STATE_LOADED:
+				break;
+
+			case PROJECT_STATE_OUTDATED:
+				question =
+					"The project file was changed after the last indexing. The project needs to get fully reindexed to "
+					"reflect the current project state. Do you want to reindex the project?";
+				forceRefresh = true;
+				break;
+
+			case PROJECT_STATE_OUTVERSIONED:
+				question =
+					"This project was indexed with a different version of Coati. It needs to be fully reindexed to be used "
+					"with this version of Coati. Do you want to reindex the project?";
+				forceRefresh = true;
+				break;
+
+			case PROJECT_STATE_SETTINGS_UPDATED:
+				question =
+					"Some settings were changed, the project needs to be fully reindexed. "
+					"Do you want to reindex the project?";
+				forceRefresh = true;
+				break;
+
+			default:
+				break;
 		}
 	}
 
+	if (forceRefresh && question.size() && Application::getInstance()->hasGUI() && !isTrial())
+	{
+		std::vector<std::string> options;
+		options.push_back("Yes");
+		options.push_back("No");
+		int result = m_dialogView->confirm(question, options);
+
+		if (result == 1)
+		{
+			return false;
+		}
+	}
+
+	if (!allowsRefresh())
+	{
+		return false;
+	}
+
+	getProjectSettings()->reload();
+
+	updateFileManager(m_fileManager);
+
+	if (buildIndex(forceRefresh))
+	{
+		m_storageAccessProxy->setSubject(m_storage.get());
+
+		m_state = PROJECT_STATE_LOADED;
+
+		return true;
+	}
+
 	return false;
 }
 
@@ -102,6 +162,14 @@ bool Project::settingsEqualExceptNameAndLocation(const ProjectSettings& otherSet
 	return getProjectSettings()->equalsExceptNameAndLocation(otherSettings);
 }
 
+void Project::setStateSettingsUpdated()
+{
+	if (m_state != PROJECT_STATE_NOT_LOADED && m_state != PROJECT_STATE_EMPTY)
+	{
+		m_state = PROJECT_STATE_SETTINGS_UPDATED;
+	}
+}
+
 void Project::logStats() const
 {
 	m_storage->logStats();
@@ -121,105 +189,57 @@ DialogView* Project::getDialogView() const
 
 void Project::load()
 {
+	m_storageAccessProxy->setSubject(nullptr);
+
 	const std::shared_ptr<ProjectSettings> projectSettings = getProjectSettings();
 	bool loadedSettings = projectSettings->reload();
-	if (loadedSettings)
+
+	if (!loadedSettings)
 	{
-		NameHierarchy::setDelimiter(getSymbolNameDelimiterForLanguage(projectSettings->getLanguage()));
-		const FilePath projectSettingsPath = projectSettings->getFilePath();
-		const FilePath dbPath = FilePath(projectSettingsPath).replaceExtension("coatidb");
-		m_storage = std::make_shared<PersistentStorage>(dbPath);
+		return;
+	}
+
+	NameHierarchy::setDelimiter(getSymbolNameDelimiterForLanguage(projectSettings->getLanguage()));
+
+	const FilePath projectSettingsPath = projectSettings->getFilePath();
+	const FilePath dbPath = FilePath(projectSettingsPath).replaceExtension("coatidb");
+
+	m_storage = std::make_shared<PersistentStorage>(dbPath);
+
+	if (m_storage->isEmpty())
+	{
+		m_state = PROJECT_STATE_EMPTY;
+		m_storage->setup();
+	}
+	else if (m_storage->isIncompatible())
+	{
+		m_state = PROJECT_STATE_OUTVERSIONED;
+	}
+	else if (TextAccess::createFromFile(projectSettingsPath.str())->getText() != m_storage->getProjectSettingsText())
+	{
+		m_state = PROJECT_STATE_OUTDATED;
+	}
+	else
+	{
+		m_state = PROJECT_STATE_LOADED;
+	}
+
+	if (m_state == PROJECT_STATE_LOADED || m_state == PROJECT_STATE_OUTDATED)
+	{
+		m_storage->finishParsing();
 		m_storageAccessProxy->setSubject(m_storage.get());
 
-		if (m_storage->isEmpty())
-		{
-			m_state = PROJECT_STATE_EMPTY;
-			m_storage->setup();
-		}
-		else if (m_storage->isIncompatible())
-		{
-			m_state = PROJECT_STATE_OUTVERSIONED;
-		}
-		else if (TextAccess::createFromFile(projectSettingsPath.str())->getText() != m_storage->getProjectSettingsText())
-		{
-			m_state = PROJECT_STATE_OUTDATED;
-		}
-		else
-		{
-			m_state = PROJECT_STATE_LOADED;
-		}
-
-		updateFileManager(m_fileManager);
-
-		bool reparse = false;
-
-		switch (m_state)
-		{
-		case PROJECT_STATE_NOT_LOADED:
-			break;
-
-		case PROJECT_STATE_EMPTY:
-			buildIndex(false);
-			m_state = PROJECT_STATE_LOADED;
-			break;
-		case PROJECT_STATE_OUTDATED:
-			if (Application::getInstance()->hasGUI() && !isTrial())
-			{
-				std::vector<std::string> options;
-				options.push_back("Yes");
-				options.push_back("No");
-				int result = Application::getInstance()->handleDialog(
-					"The project file was changed after the last indexing. The project needs to get fully reindexed to "
-					"reflect the current project state. Do you want to reindex the project?", options);
-
-				reparse = (result == 0);
-			}
-			// dont break here.
-		case PROJECT_STATE_LOADED:
-			m_storage->finishParsing();
-			MessageFinishedParsing().dispatch();
-			MessageStatus("Finished Loading", false, false).dispatch();
-			break;
-		case PROJECT_STATE_OUTVERSIONED:
-			MessageStatus("Can't load project").dispatch();
-
-			reparse = true;
-
-			if (Application::getInstance()->hasGUI() && !isTrial())
-			{
-				std::vector<std::string> options;
-				options.push_back("Yes");
-				options.push_back("No");
-				int result = Application::getInstance()->handleDialog(
-					"This project was indexed with a different version of Coati. It needs to be fully reindexed to be used "
-					"with this version of Coati. Do you want to reindex the project?", options);
-
-				reparse = (result == 0);
-			}
-			m_storage.reset();
-			break;
-		}
-
-		if (reparse)
-		{
-			refresh(true);
-		}
+		MessageFinishedParsing().dispatch();
+		MessageStatus("Finished Loading", false, false).dispatch();
 	}
-}
-
-void Project::clearStorage()
-{
-	if (!m_storage)
+	else
 	{
-		const FilePath projectSettingsPath = getProjectSettings()->getFilePath();
-		const FilePath dbPath = FilePath(projectSettingsPath).replaceExtension("coatidb");
-		m_storage = std::make_shared<PersistentStorage>(dbPath);
+		MessageStatus("Project not loaded", false, false).dispatch();
 	}
 
-	if (m_storage)
+	if (m_state != PROJECT_STATE_LOADED)
 	{
-		m_storage->clear();
-		m_state = PROJECT_STATE_EMPTY;
+		MessageRefresh().dispatch();
 	}
 }
 
@@ -266,7 +286,7 @@ bool Project::buildIndex(bool forceRefresh)
 
 	if (forceRefresh)
 	{
-		clearStorage();
+		m_storage->clear();
 	}
 
 	m_storage->setProjectSettingsText(TextAccess::createFromFile(getProjectSettingsFilePath().str())->getText());
@@ -309,5 +329,3 @@ bool Project::allowsRefresh()
 {
 	return true;
 }
-
-
diff --git a/src/lib/Project.h b/src/lib/Project.h
index b2794965..cbb49d76 100644
--- a/src/lib/Project.h
+++ b/src/lib/Project.h
@@ -7,13 +7,14 @@
 #include "utility/file/FileManager.h"
 
 #include "data/parser/Parser.h"
-#include "settings/ProjectSettings.h" // todo: use forward declaration here
-#include "utility/scheduling/Task.h"
+#include "settings/LanguageType.h"
 
 class DialogView;
-class PersistentStorage;
-class StorageAccessProxy;
 class FileRegister;
+class PersistentStorage;
+class ProjectSettings;
+class StorageAccessProxy;
+class Task;
 
 class Project
 {
@@ -28,7 +29,10 @@ public:
 	FilePath getProjectSettingsFilePath() const;
 	LanguageType getLanguage() const;
 	std::string getDescription() const;
+
 	bool settingsEqualExceptNameAndLocation(const ProjectSettings& otherSettings) const;
+	void setStateSettingsUpdated();
+
 	void logStats() const;
 
 protected:
@@ -45,13 +49,13 @@ private:
 		PROJECT_STATE_EMPTY,
 		PROJECT_STATE_LOADED,
 		PROJECT_STATE_OUTDATED,
-		PROJECT_STATE_OUTVERSIONED
+		PROJECT_STATE_OUTVERSIONED,
+		PROJECT_STATE_SETTINGS_UPDATED
 	};
 
 	Project(const Project&);
 
 	void load();
-	void clearStorage();
 	bool buildIndex(bool forceRefresh);
 
 	virtual bool allowsRefresh();
diff --git a/src/lib_gui/qt/element/QtCodeFile.cpp b/src/lib_gui/qt/element/QtCodeFile.cpp
index 9b0f10d8..d060be1b 100644
--- a/src/lib_gui/qt/element/QtCodeFile.cpp
+++ b/src/lib_gui/qt/element/QtCodeFile.cpp
@@ -21,7 +21,6 @@
 
 QtCodeFile::QtCodeFile(const FilePath& filePath, QtCodeNavigator* navigator)
 	: QFrame()
-	, m_updateTitleBarFunctor(std::bind(&QtCodeFile::doUpdateTitleBar, this))
 	, m_navigator(navigator)
 	, m_filePath(filePath)
 	, m_contentRequested(false)
@@ -403,6 +402,27 @@ void QtCodeFile::updateSnippets()
 	m_snippets.back()->setProperty("isLast", true);
 }
 
+void QtCodeFile::updateTitleBar()
+{
+	if (isTrial())
+	{
+		return;
+	}
+
+	// cannot use m_filePath.exists() here since it is only checked when FilePath is constructed.
+	if ((!FileSystem::exists(m_filePath.str())) ||
+		(FileSystem::getLastWriteTime(m_filePath) > m_modificationTime))
+	{
+		m_title->setText(QString(m_filePath.fileName().c_str()) + "*");
+		m_title->setToolTip(QString::fromStdString("out of date: " + m_filePath.str()));
+	}
+	else
+	{
+		m_title->setText(m_filePath.fileName().c_str());
+		m_title->setToolTip(QString::fromStdString(m_filePath.str()));
+	}
+}
+
 void QtCodeFile::clickedMinimizeButton() const
 {
 	MessageChangeFileView(
@@ -459,11 +479,6 @@ void QtCodeFile::editProject()
 	MessageProjectEdit().dispatch();
 }
 
-void QtCodeFile::handleMessage(MessageWindowFocus* message)
-{
-	updateTitleBar();
-}
-
 void QtCodeFile::updateRefCount(int refCount)
 {
 	if (refCount > 0)
@@ -488,29 +503,3 @@ void QtCodeFile::updateRefCount(int refCount)
 		m_referenceCount->hide();
 	}
 }
-
-void QtCodeFile::updateTitleBar()
-{
-	m_updateTitleBarFunctor();
-}
-
-void QtCodeFile::doUpdateTitleBar()
-{
-	if (isTrial())
-	{
-		return;
-	}
-
-	// cannot use m_filePath.exists() here since it is only checked when FilePath is constructed.
-	if ((!FileSystem::exists(m_filePath.str())) ||
-		(FileSystem::getLastWriteTime(m_filePath) > m_modificationTime))
-	{
-		m_title->setText(QString(m_filePath.fileName().c_str()) + "*");
-		m_title->setToolTip(QString::fromStdString("out of date: " + m_filePath.str()));
-	}
-	else
-	{
-		m_title->setText(m_filePath.fileName().c_str());
-		m_title->setToolTip(QString::fromStdString(m_filePath.str()));
-	}
-}
diff --git a/src/lib_gui/qt/element/QtCodeFile.h b/src/lib_gui/qt/element/QtCodeFile.h
index 37975257..e21cdbb4 100644
--- a/src/lib_gui/qt/element/QtCodeFile.h
+++ b/src/lib_gui/qt/element/QtCodeFile.h
@@ -10,9 +10,6 @@
 #include "utility/file/FilePath.h"
 #include "utility/TimePoint.h"
 #include "utility/types.h"
-#include "utility/messaging/MessageListener.h"
-#include "utility/messaging/type/MessageWindowFocus.h"
-#include "qt/utility/QtThreadedFunctor.h"
 
 #include "data/ErrorInfo.h"
 #include "component/view/helper/CodeSnippetParams.h"
@@ -26,7 +23,6 @@ class TokenLocationFile;
 
 class QtCodeFile
 	: public QFrame
-	, MessageListener<MessageWindowFocus>
 {
 	Q_OBJECT
 
@@ -59,6 +55,7 @@ public:
 
 	bool hasSnippets() const;
 	void updateSnippets();
+	void updateTitleBar();
 
 public slots:
 	void clickedMinimizeButton() const;
@@ -71,13 +68,7 @@ private slots:
 	void editProject();
 
 private:
-	virtual void handleMessage(MessageWindowFocus* message);
-
 	void updateRefCount(int refCount);
-	void updateTitleBar();
-	void doUpdateTitleBar();
-
-	QtThreadedFunctor<> m_updateTitleBarFunctor;
 
 	QtCodeNavigator* m_navigator;
 
diff --git a/src/lib_gui/qt/element/QtCodeFileList.cpp b/src/lib_gui/qt/element/QtCodeFileList.cpp
index 90358172..aa2d3d32 100644
--- a/src/lib_gui/qt/element/QtCodeFileList.cpp
+++ b/src/lib_gui/qt/element/QtCodeFileList.cpp
@@ -93,6 +93,14 @@ void QtCodeFileList::showContents()
 	}
 }
 
+void QtCodeFileList::onWindowFocus()
+{
+	for (std::shared_ptr<QtCodeFile> filePtr : m_files)
+	{
+		filePtr->updateTitleBar();
+	}
+}
+
 QtCodeFile* QtCodeFileList::getFile(const FilePath filePath)
 {
 	QtCodeFile* file = nullptr;
diff --git a/src/lib_gui/qt/element/QtCodeFileList.h b/src/lib_gui/qt/element/QtCodeFileList.h
index 9ddeeab1..8ab88445 100644
--- a/src/lib_gui/qt/element/QtCodeFileList.h
+++ b/src/lib_gui/qt/element/QtCodeFileList.h
@@ -41,6 +41,8 @@ public:
 	void updateFiles();
 	void showContents();
 
+	void onWindowFocus();
+
 	QtCodeFile* getFile(const FilePath filePath);
 
 private:
diff --git a/src/lib_gui/qt/element/QtCodeNavigator.cpp b/src/lib_gui/qt/element/QtCodeNavigator.cpp
index 59f0bc2b..b361f695 100644
--- a/src/lib_gui/qt/element/QtCodeNavigator.cpp
+++ b/src/lib_gui/qt/element/QtCodeNavigator.cpp
@@ -20,7 +20,6 @@
 
 QtCodeNavigator::QtCodeNavigator(QWidget* parent)
 	: QWidget(parent)
-	, m_switchReferenceFunctor(std::bind(&QtCodeNavigator::doSwitchReference, this, std::placeholders::_1))
 	, m_value(0)
 	, m_refIndex(0)
 	, m_scrollToFile(nullptr)
@@ -602,17 +601,29 @@ void QtCodeNavigator::ensureWidgetVisibleAnimated(QWidget *childWidget, QRectF r
 
 void QtCodeNavigator::handleMessage(MessageCodeReference* message)
 {
-	m_switchReferenceFunctor(message->type);
+	MessageCodeReference::ReferenceType type = message->type;
+
+	m_onQtThread(
+		[=]()
+		{
+			if (type == MessageCodeReference::REFERENCE_PREVIOUS)
+			{
+				previousReference();
+			}
+			else if (type == MessageCodeReference::REFERENCE_NEXT)
+			{
+				nextReference();
+			}
+		}
+	);
 }
 
-void QtCodeNavigator::doSwitchReference(MessageCodeReference::ReferenceType type)
+void QtCodeNavigator::handleMessage(MessageWindowFocus* message)
 {
-	if (type == MessageCodeReference::REFERENCE_PREVIOUS)
-	{
-		previousReference();
-	}
-	else if (type == MessageCodeReference::REFERENCE_NEXT)
-	{
-		nextReference();
-	}
+	m_onQtThread(
+		[=]()
+		{
+			m_list->onWindowFocus();
+		}
+	);
 }
diff --git a/src/lib_gui/qt/element/QtCodeNavigator.h b/src/lib_gui/qt/element/QtCodeNavigator.h
index a8519ef9..49e029e3 100644
--- a/src/lib_gui/qt/element/QtCodeNavigator.h
+++ b/src/lib_gui/qt/element/QtCodeNavigator.h
@@ -9,6 +9,7 @@
 #include "qt/utility/QtThreadedFunctor.h"
 #include "utility/messaging/MessageListener.h"
 #include "utility/messaging/type/MessageCodeReference.h"
+#include "utility/messaging/type/MessageWindowFocus.h"
 
 class QLabel;
 class QPushButton;
@@ -18,6 +19,7 @@ class TokenLocationFile;
 class QtCodeNavigator
 	: public QWidget
 	, public MessageListener<MessageCodeReference>
+	, public MessageListener<MessageWindowFocus>
 {
 	Q_OBJECT
 
@@ -99,9 +101,9 @@ private:
 	void ensureWidgetVisibleAnimated(QWidget *childWidget, QRectF rect);
 
 	void handleMessage(MessageCodeReference* message);
-	void doSwitchReference(MessageCodeReference::ReferenceType type);
+	void handleMessage(MessageWindowFocus* message);
 
-	QtThreadedFunctor<MessageCodeReference::ReferenceType> m_switchReferenceFunctor;
+	QtThreadedLambdaFunctor m_onQtThread;
 
 	QScrollArea* m_scrollArea;
 	QtCodeFileList* m_list;
diff --git a/src/test/CMakeLists.txt b/src/test/CMakeLists.txt
index 663a50bb..859ca4d0 100644
--- a/src/test/CMakeLists.txt
+++ b/src/test/CMakeLists.txt
@@ -15,7 +15,7 @@ add_files(
 	FileSystemTestSuite.h
 	GeneratorTestSuite.h
 	GraphTestSuite.h
-	JavaParserTestSuite.h
+#	JavaParserTestSuite.h
 	LogManagerTestSuite.h
 	MatrixBaseTestSuite.h
 	MessageQueueTestSuite.h