diff --git a/src/lib/component/view/DialogView.cpp b/src/lib/component/view/DialogView.cpp
index 906d613e..a915767d 100644
--- a/src/lib/component/view/DialogView.cpp
+++ b/src/lib/component/view/DialogView.cpp
@@ -42,7 +42,7 @@ void DialogView::hideProgressDialog()
 }
 
 void DialogView::startIndexingDialog(
-	Project* project, const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode,
+	Project* project, const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode, bool enabledShallowOption, bool shallow, 
 	std::function<void(const RefreshInfo& info)> onStartIndexing, std::function<void()> onCancelIndexing)
 {
 }
@@ -59,7 +59,7 @@ void DialogView::updateCustomIndexingDialog(
 
 DatabasePolicy DialogView::finishedIndexingDialog(
 	size_t indexedFileCount, size_t totalIndexedFileCount, size_t completedFileCount, size_t totalFileCount,
-	float time, ErrorCountInfo errorInfo, bool interrupted)
+	float time, ErrorCountInfo errorInfo, bool interrupted, bool shallow)
 {
 	return DATABASE_POLICY_KEEP; // used in non-gui mode
 }
diff --git a/src/lib/component/view/DialogView.h b/src/lib/component/view/DialogView.h
index d7fbb719..ef8bee71 100644
--- a/src/lib/component/view/DialogView.h
+++ b/src/lib/component/view/DialogView.h
@@ -15,6 +15,7 @@ enum DatabasePolicy
 {
 	DATABASE_POLICY_KEEP,
 	DATABASE_POLICY_DISCARD,
+	DATABASE_POLICY_REFRESH,
 	DATABASE_POLICY_UNKNOWN
 };
 
@@ -45,7 +46,7 @@ public:
 	virtual void hideProgressDialog();
 
 	virtual void startIndexingDialog(
-		Project* project, const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode,
+		Project* project, const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode, bool enabledShallowOption, bool shallow,
 		std::function<void(const RefreshInfo& info)> onStartIndexing, std::function<void()> onCancelIndexing);
 	virtual void updateIndexingDialog(
 		size_t startedFileCount, size_t finishedFileCount, size_t totalFileCount, const std::vector<FilePath>& sourcePaths);
@@ -53,7 +54,7 @@ public:
 		size_t startedFileCount, size_t finishedFileCount, size_t totalFileCount, const std::vector<FilePath>& sourcePaths);
 	virtual DatabasePolicy finishedIndexingDialog(
 		size_t indexedFileCount, size_t totalIndexedFileCount, size_t completedFileCount, size_t totalFileCount,
-		float time, ErrorCountInfo errorInfo, bool interrupted);
+		float time, ErrorCountInfo errorInfo, bool interrupted, bool shallow);
 
 	int confirm(const std::wstring& message);
 	virtual int confirm(const std::wstring& message, const std::vector<std::wstring>& options);
diff --git a/src/lib/data/TaskFinishParsing.cpp b/src/lib/data/TaskFinishParsing.cpp
index 277eaf6f..f587a4e0 100644
--- a/src/lib/data/TaskFinishParsing.cpp
+++ b/src/lib/data/TaskFinishParsing.cpp
@@ -61,6 +61,9 @@ Task::TaskState TaskFinishParsing::doUpdate(std::shared_ptr<Blackboard> blackboa
 	bool interruptedIndexing = false;
 	blackboard->get("interrupted_indexing", interruptedIndexing);
 
+	bool shallowIndexing = false;
+	blackboard->get("shallow_indexing", shallowIndexing);
+
 	ErrorCountInfo errorInfo = m_storage->getErrorCount();
 
 	std::wstring status;
@@ -82,7 +85,8 @@ Task::TaskState TaskFinishParsing::doUpdate(std::shared_ptr<Blackboard> blackboa
 		stats.fileCount,
 		time,
 		errorInfo,
-		interruptedIndexing
+		interruptedIndexing,
+		shallowIndexing
 	);
 
 	MessageIndexingStatus(false).dispatch();
@@ -95,6 +99,11 @@ Task::TaskState TaskFinishParsing::doUpdate(std::shared_ptr<Blackboard> blackboa
 	{
 		blackboard->set("discard_database", true);
 	}
+	else if (policy == DATABASE_POLICY_REFRESH)
+	{
+		blackboard->set("keep_database", true);
+		blackboard->set("refresh_database", true);
+	}
 
 	return STATE_SUCCESS;
 }
diff --git a/src/lib/data/indexer/TaskExecuteCustomCommands.cpp b/src/lib/data/indexer/TaskExecuteCustomCommands.cpp
index 4a89976b..2813cf2f 100644
--- a/src/lib/data/indexer/TaskExecuteCustomCommands.cpp
+++ b/src/lib/data/indexer/TaskExecuteCustomCommands.cpp
@@ -260,7 +260,7 @@ void TaskExecuteCustomCommands::runPythonPostProcessing(PersistentStorage& stora
 	std::vector<Id> unsolvedLocationIds;
 	for (const StorageSourceLocation location : storage.getStorageSourceLocations())
 	{
-		if (intToLocationType(location.type) == LOCATION_UNSOLVED)
+		if (intToLocationType(location.type) == LOCATION_UNSOLVED) // FIXME: this doesn't catch unsolved qualifiers -> convert Qualifier location type to qualifier edge
 		{
 			unsolvedLocationIds.push_back(location.id);
 		}
@@ -286,9 +286,9 @@ void TaskExecuteCustomCommands::runPythonPostProcessing(PersistentStorage& stora
 	storage.setMode(SqliteIndexStorage::STORAGE_MODE_READ);
 
 	std::vector<DataToInsert> dataToInsert;
-	std::set<Id> elementsToDelete;
+	std::vector<StorageOccurrence> occurrencesToDelete;
 	locationCollection->forEachSourceLocationFile(
-		[&nodeNameToStorageNodes, &storage, &dataToInsert, &elementsToDelete](std::shared_ptr<SourceLocationFile> locationFile)
+		[&nodeNameToStorageNodes, &storage, &dataToInsert, &occurrencesToDelete](std::shared_ptr<SourceLocationFile> locationFile)
 		{
 			const FilePath filePath = locationFile->getFilePath();
 			if (filePath.empty())
@@ -305,7 +305,7 @@ void TaskExecuteCustomCommands::runPythonPostProcessing(PersistentStorage& stora
 			if (textAccess)
 			{
 				locationFile->forEachStartSourceLocation(
-					[textAccess, &nodeNameToStorageNodes, &storage, &dataToInsert, &elementsToDelete](const SourceLocation* startLoc)
+					[textAccess, &nodeNameToStorageNodes, &storage, &dataToInsert, &occurrencesToDelete](const SourceLocation* startLoc)
 					{
 						if (!startLoc)
 						{
@@ -319,23 +319,20 @@ void TaskExecuteCustomCommands::runPythonPostProcessing(PersistentStorage& stora
 
 						const std::wstring token = utility::decodeFromUtf8(textAccess->getLine(startLoc->getLineNumber()).substr(startLoc->getColumnNumber() - 1, endLoc->getColumnNumber() - startLoc->getColumnNumber() + 1));
 
-						for (const Id tokenId : startLoc->getTokenIds())
+						for (const Id elementId : startLoc->getTokenIds())
 						{
-							const StorageEdge edge = storage.getEdgeById(tokenId);
+							const StorageEdge edge = storage.getEdgeById(elementId);
 							if (edge.id != 0)
 							{
 								for (const StorageNode& targetNode : nodeNameToStorageNodes[token])
 								{
-									if (Edge::intToType(edge.type) == Edge::EDGE_CALL &&
-										(
-											NodeType::intToType(targetNode.type) != NodeType::NODE_FUNCTION ||
-											NodeType::intToType(targetNode.type) != NodeType::NODE_METHOD
-										)
-									){
+									if (Edge::intToType(edge.type) == Edge::EDGE_INHERITANCE &&
+										NodeType::intToType(targetNode.type) != NodeType::NODE_CLASS)
+									{
 										continue;
 									}
 									dataToInsert.push_back({ StorageEdgeData(edge.type, edge.sourceNodeId, targetNode.id) , startLoc->getLocationId() });
-									elementsToDelete.insert(edge.id);
+									occurrencesToDelete.push_back(StorageOccurrence(edge.id, startLoc->getLocationId()));
 								}
 							}
 						}
@@ -364,7 +361,15 @@ void TaskExecuteCustomCommands::runPythonPostProcessing(PersistentStorage& stora
 			storage.addOccurrence(StorageOccurrence(ambiguousEdgeIds[i], dataToInsert[i].sourceLocationId));
 		}
 		storage.setMode(SqliteIndexStorage::STORAGE_MODE_CLEAR);
-		storage.removeElements(utility::toVector(elementsToDelete));
+
+		storage.removeOccurrences(occurrencesToDelete);
+		std::set<Id> edgeIds;
+		for (const StorageOccurrence& occurrence : occurrencesToDelete)
+		{
+			edgeIds.insert(occurrence.elementId);
+		}
+		storage.removeElementsWithoutOccurrences(utility::toVector(edgeIds));
+
 		storage.finishInjection();
 		LOG_INFO("Finished Python post processing.");
 	}
diff --git a/src/lib/data/storage/PersistentStorage.cpp b/src/lib/data/storage/PersistentStorage.cpp
index 5a74e0bf..7573672f 100644
--- a/src/lib/data/storage/PersistentStorage.cpp
+++ b/src/lib/data/storage/PersistentStorage.cpp
@@ -165,6 +165,21 @@ void PersistentStorage::removeElements(const std::vector<Id>& ids)
 	m_sqliteIndexStorage.removeElements(ids);
 }
 
+void PersistentStorage::removeOccurrence(const StorageOccurrence& occurrence)
+{
+	m_sqliteIndexStorage.removeOccurrence(occurrence);
+}
+
+void PersistentStorage::removeOccurrences(const std::vector<StorageOccurrence>& occurrences)
+{
+	m_sqliteIndexStorage.removeOccurrences(occurrences);
+}
+
+void PersistentStorage::removeElementsWithoutOccurrences(const std::vector<Id>& elementIds)
+{
+	m_sqliteIndexStorage.removeElementsWithoutOccurrences(elementIds);
+}
+
 const std::vector<StorageNode>& PersistentStorage::getStorageNodes() const
 {
 	return m_storageData.nodes = m_sqliteIndexStorage.getAll<StorageNode>();
diff --git a/src/lib/data/storage/PersistentStorage.h b/src/lib/data/storage/PersistentStorage.h
index 738659a2..acf0ba87 100644
--- a/src/lib/data/storage/PersistentStorage.h
+++ b/src/lib/data/storage/PersistentStorage.h
@@ -40,6 +40,9 @@ public:
 
 	void removeElement(const Id id);
 	void removeElements(const std::vector<Id>& ids);
+	void removeOccurrence(const StorageOccurrence& occurrence);
+	void removeOccurrences(const std::vector<StorageOccurrence>& occurrences);
+	void removeElementsWithoutOccurrences(const std::vector<Id>& elementIds);
 
 	const std::vector<StorageNode>& getStorageNodes() const override;
 	const std::vector<StorageFile>& getStorageFiles() const override;
diff --git a/src/lib/data/storage/sqlite/SqliteIndexStorage.cpp b/src/lib/data/storage/sqlite/SqliteIndexStorage.cpp
index 3b08daa3..41f9c722 100644
--- a/src/lib/data/storage/sqlite/SqliteIndexStorage.cpp
+++ b/src/lib/data/storage/sqlite/SqliteIndexStorage.cpp
@@ -477,6 +477,28 @@ void SqliteIndexStorage::removeElements(const std::vector<Id>& ids)
 	);
 }
 
+void SqliteIndexStorage::removeOccurrence(const StorageOccurrence& occurrence)
+{
+	executeStatement(
+		"DELETE FROM occurrence WHERE element_id = " + std::to_string(occurrence.elementId) + " AND source_location_id = " + std::to_string(occurrence.sourceLocationId) + ";"
+	);
+}
+
+void SqliteIndexStorage::removeOccurrences(const std::vector<StorageOccurrence>& occurrences)
+{
+	for (const StorageOccurrence& occurrence : occurrences)
+	{
+		removeOccurrence(occurrence);
+	}
+}
+
+void SqliteIndexStorage::removeElementsWithoutOccurrences(const std::vector<Id>& elementIds)
+{
+	executeStatement(
+		"DELETE FROM element WHERE id IN (" + utility::join(utility::toStrings(elementIds), ',') + ") AND id NOT IN (SELECT element_id FROM occurrence);"
+	);
+}
+
 void SqliteIndexStorage::removeElementsWithLocationInFiles(
 	const std::vector<Id>& fileIds, std::function<void(int)> updateStatusCallback)
 {
diff --git a/src/lib/data/storage/sqlite/SqliteIndexStorage.h b/src/lib/data/storage/sqlite/SqliteIndexStorage.h
index da04ccae..b24a97ce 100644
--- a/src/lib/data/storage/sqlite/SqliteIndexStorage.h
+++ b/src/lib/data/storage/sqlite/SqliteIndexStorage.h
@@ -72,6 +72,9 @@ public:
 
 	void removeElement(Id id);
 	void removeElements(const std::vector<Id>& ids);
+	void removeOccurrence(const StorageOccurrence& occurrence);
+	void removeOccurrences(const std::vector<StorageOccurrence>& occurrences);
+	void removeElementsWithoutOccurrences(const std::vector<Id>& elementIds);
 	void removeElementsWithLocationInFiles(const std::vector<Id>& fileIds, std::function<void(int)> updateStatusCallback);
 
 	void removeAllErrors();
diff --git a/src/lib/project/Project.cpp b/src/lib/project/Project.cpp
index 59fb95dd..293909ac 100644
--- a/src/lib/project/Project.cpp
+++ b/src/lib/project/Project.cpp
@@ -26,6 +26,7 @@
 #include "FileSystem.h"
 #include "MessageErrorCountClear.h"
 #include "MessageIndexingFinished.h"
+#include "MessageIndexingShowDialog.h"
 #include "MessageIndexingStarted.h"
 #include "MessageIndexingStatus.h"
 #include "MessageRefresh.h"
@@ -73,14 +74,14 @@ bool Project::isLoaded() const
 {
 	switch (m_state)
 	{
-		case PROJECT_STATE_EMPTY:
-		case PROJECT_STATE_LOADED:
-		case PROJECT_STATE_OUTDATED:
-		case PROJECT_STATE_NEEDS_MIGRATION:
-			return true;
+	case PROJECT_STATE_EMPTY:
+	case PROJECT_STATE_LOADED:
+	case PROJECT_STATE_OUTDATED:
+	case PROJECT_STATE_NEEDS_MIGRATION:
+		return true;
 
-		default:
-			break;
+	default:
+		break;
 	}
 
 	return false;
@@ -354,6 +355,18 @@ void Project::refresh(RefreshMode refreshMode, std::shared_ptr<DialogView> dialo
 		refreshMode = REFRESH_UPDATED_FILES;
 	}
 
+	bool allowsShallowIndexing = false;
+	for (const std::shared_ptr<SourceGroup>& sourceGroup : m_sourceGroups)
+	{
+		if (sourceGroup->getStatus() == SOURCE_GROUP_STATUS_ENABLED && sourceGroup->allowsShallowIndexing())
+		{
+			allowsShallowIndexing = true;
+			break;
+		}
+	}
+
+	const bool useShallowIndexing = allowsShallowIndexing && (!isLoaded() || m_state == PROJECT_STATE_EMPTY);
+
 	if (m_hasGUI)
 	{
 		std::vector<RefreshMode> enabledModes = { REFRESH_ALL_FILES };
@@ -362,7 +375,7 @@ void Project::refresh(RefreshMode refreshMode, std::shared_ptr<DialogView> dialo
 			enabledModes.insert(enabledModes.end(), { REFRESH_UPDATED_FILES, REFRESH_UPDATED_AND_INCOMPLETE_FILES });
 		}
 
-		dialogView->startIndexingDialog(this, enabledModes, refreshMode,
+		dialogView->startIndexingDialog(this, enabledModes, refreshMode, allowsShallowIndexing, useShallowIndexing,
 			[this, dialogView](const RefreshInfo& info)
 			{
 				buildIndex(info, dialogView);
@@ -453,7 +466,9 @@ void Project::buildIndex(RefreshInfo info, std::shared_ptr<DialogView> dialogVie
 					}
 					else
 					{
+						const bool shallow = info.shallow;
 						info = getRefreshInfo(REFRESH_ALL_FILES);
+						info.shallow = shallow;
 					}
 				}
 
@@ -476,6 +491,7 @@ void Project::buildIndex(RefreshInfo info, std::shared_ptr<DialogView> dialogVie
 
 	if (info.mode != REFRESH_ALL_FILES)
 	{
+		// store the indexed data into the temp db but keep the current state to allow browsing while indexing
 		FileSystem::copyFile(indexDbFilePath, tempIndexDbFilePath);
 	}
 
@@ -507,17 +523,18 @@ void Project::buildIndex(RefreshInfo info, std::shared_ptr<DialogView> dialogVie
 			if (sourceGroup->getType() == SOURCE_GROUP_CUSTOM_COMMAND ||
 				sourceGroup->getType() == SOURCE_GROUP_PYTHON_EMPTY)
 			{
-				customIndexerCommandProvider->addProvider(sourceGroup->getIndexerCommandProvider(info.filesToIndex));
+				customIndexerCommandProvider->addProvider(sourceGroup->getIndexerCommandProvider(info));
 			}
 			else
 			{
-				indexerCommandProvider->addProvider(sourceGroup->getIndexerCommandProvider(info.filesToIndex));
+				indexerCommandProvider->addProvider(sourceGroup->getIndexerCommandProvider(info));
 			}
 		}
 	}
 
 	size_t sourceFileCount = indexerCommandProvider->size() + customIndexerCommandProvider->size();
 
+	taskSequential->addTask(std::make_shared<TaskSetValue<bool>>("shallow_indexing", info.shallow));
 	taskSequential->addTask(std::make_shared<TaskSetValue<int>>("source_file_count", sourceFileCount));
 	taskSequential->addTask(std::make_shared<TaskSetValue<int>>("indexed_source_file_count", 0));
 	taskSequential->addTask(std::make_shared<TaskSetValue<bool>>("interrupted_indexing", false));
@@ -670,6 +687,24 @@ void Project::buildIndex(RefreshInfo info, std::shared_ptr<DialogView> dialogVie
 		MessageIndexingFinished().dispatch();
 	}));
 
+	taskSequential->addTask(std::make_shared<TaskGroupSelector>()->addChildTasks(
+		std::make_shared<TaskGroupSequence>()->addChildTasks(
+			std::make_shared<TaskFindKeyOnBlackboard>("refresh_database"),
+			std::make_shared<TaskLambda>([dialogView, this]() {
+				Task::dispatch(TabId::app(), std::make_shared<TaskLambda>([dialogView, this]() {
+					MessageIndexingShowDialog().dispatch();
+					MessageRefresh().refreshAll().dispatch();
+				}));
+			})
+		),
+		std::make_shared<TaskGroupSequence>()->addChildTasks(
+			std::make_shared<TaskLambda>([this]() {
+				Task::dispatch(TabId::app(), std::make_shared<TaskLambda>([this]() {
+				}));
+			})
+		)
+	));
+
 	taskSequential->setIsBackgroundTask(true);
 	Task::dispatch(TabId::app(), taskSequential);
 
diff --git a/src/lib/project/RefreshInfo.h b/src/lib/project/RefreshInfo.h
index e8962bee..4c468761 100644
--- a/src/lib/project/RefreshInfo.h
+++ b/src/lib/project/RefreshInfo.h
@@ -20,6 +20,7 @@ struct RefreshInfo
 	std::set<FilePath> nonIndexedFilesToClear;
 
 	RefreshMode mode = REFRESH_NONE;
+	bool shallow = true;
 };
 
 #endif // REFRESH_INFO_H
diff --git a/src/lib/project/SourceGroup.cpp b/src/lib/project/SourceGroup.cpp
index ed80ae70..3bc750ad 100644
--- a/src/lib/project/SourceGroup.cpp
+++ b/src/lib/project/SourceGroup.cpp
@@ -7,9 +7,9 @@
 #include "SourceGroupSettings.h"
 #include "TaskLambda.h"
 
-std::shared_ptr<IndexerCommandProvider> SourceGroup::getIndexerCommandProvider(const std::set<FilePath>& filesToIndex) const
+std::shared_ptr<IndexerCommandProvider> SourceGroup::getIndexerCommandProvider(const RefreshInfo& info) const
 {
-	return std::make_shared<MemoryIndexerCommandProvider>(getIndexerCommands(filesToIndex));
+	return std::make_shared<MemoryIndexerCommandProvider>(getIndexerCommands(info));
 }
 
 std::shared_ptr<Task> SourceGroup::getPreIndexTask(
@@ -43,6 +43,11 @@ bool SourceGroup::allowsPartialClearing() const
 	return true;
 }
 
+bool SourceGroup::allowsShallowIndexing() const
+{
+	return false;
+}
+
 std::set<FilePath> SourceGroup::filterToContainedSourceFilePath(const std::set<FilePath>& sourceFilePaths) const
 {
 	std::set<FilePath> filteredSourceFilePaths;
diff --git a/src/lib/project/SourceGroup.h b/src/lib/project/SourceGroup.h
index 49e97b02..e79981b2 100644
--- a/src/lib/project/SourceGroup.h
+++ b/src/lib/project/SourceGroup.h
@@ -18,6 +18,8 @@ class SourceGroupSettings;
 class StorageProvider;
 class Task;
 
+struct RefreshInfo;
+
 class SourceGroup
 {
 public:
@@ -25,11 +27,12 @@ public:
 
 	virtual bool prepareIndexing();
 	virtual bool allowsPartialClearing() const;
+	virtual bool allowsShallowIndexing() const;
 
 	virtual std::set<FilePath> filterToContainedFilePaths(const std::set<FilePath>& filePaths) const = 0;
 	virtual std::set<FilePath> getAllSourceFilePaths() const = 0;
-	virtual std::shared_ptr<IndexerCommandProvider> getIndexerCommandProvider(const std::set<FilePath>& filesToIndex) const;
-	virtual std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const std::set<FilePath>& filesToIndex) const = 0;
+	virtual std::shared_ptr<IndexerCommandProvider> getIndexerCommandProvider(const RefreshInfo& info) const;
+	virtual std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const RefreshInfo& info) const = 0;
 	virtual std::shared_ptr<Task> getPreIndexTask(
 		std::shared_ptr<StorageProvider> storageProvider, std::shared_ptr<DialogView> dialogView) const;
 
diff --git a/src/lib/project/SourceGroupCustomCommand.cpp b/src/lib/project/SourceGroupCustomCommand.cpp
index 98040cb3..b0d81604 100644
--- a/src/lib/project/SourceGroupCustomCommand.cpp
+++ b/src/lib/project/SourceGroupCustomCommand.cpp
@@ -3,6 +3,7 @@
 #include "FileManager.h"
 #include "IndexerCommandCustom.h"
 #include "ProjectSettings.h"
+#include "RefreshInfo.h"
 #include "SourceGroupSettingsCustomCommand.h"
 #include "SqliteIndexStorage.h"
 #include "utility.h"
@@ -38,7 +39,7 @@ std::set<FilePath> SourceGroupCustomCommand::getAllSourceFilePaths() const
 	return fileManager.getAllSourceFilePaths();
 }
 
-std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCustomCommand::getIndexerCommands(const std::set<FilePath>& filesToIndex) const
+std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCustomCommand::getIndexerCommands(const RefreshInfo& info) const
 {
 	const std::wstring customCommand = m_settings->getCustomCommand();
 	const bool runInParallel = m_settings->getRunInParallel();
@@ -46,7 +47,7 @@ std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCustomCommand::getIndexe
 	std::vector<std::shared_ptr<IndexerCommand>> indexerCommands;
 	for (const FilePath& sourcePath: getAllSourceFilePaths())
 	{
-		if (filesToIndex.find(sourcePath) != filesToIndex.end())
+		if (info.filesToIndex.find(sourcePath) != info.filesToIndex.end())
 		{
 			indexerCommands.push_back(std::make_shared<IndexerCommandCustom>(
 				customCommand, 
diff --git a/src/lib/project/SourceGroupCustomCommand.h b/src/lib/project/SourceGroupCustomCommand.h
index 1fc4c0c6..20271067 100644
--- a/src/lib/project/SourceGroupCustomCommand.h
+++ b/src/lib/project/SourceGroupCustomCommand.h
@@ -18,7 +18,7 @@ public:
 
 	std::set<FilePath> filterToContainedFilePaths(const std::set<FilePath>& filePaths) const override;
 	std::set<FilePath> getAllSourceFilePaths() const override;
-	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const std::set<FilePath>& filesToIndex) const override;
+	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const RefreshInfo& info) const override;
 
 private:
 	std::shared_ptr<SourceGroupSettings> getSourceGroupSettings() override;
diff --git a/src/lib_cxx/project/SourceGroupCxxCdb.cpp b/src/lib_cxx/project/SourceGroupCxxCdb.cpp
index f44b8ad7..06d8e8bb 100644
--- a/src/lib_cxx/project/SourceGroupCxxCdb.cpp
+++ b/src/lib_cxx/project/SourceGroupCxxCdb.cpp
@@ -80,7 +80,7 @@ std::set<FilePath> SourceGroupCxxCdb::getAllSourceFilePaths(std::shared_ptr<clan
 	return sourceFilePaths;
 }
 
-std::shared_ptr<IndexerCommandProvider> SourceGroupCxxCdb::getIndexerCommandProvider(const std::set<FilePath>& filesToIndex) const
+std::shared_ptr<IndexerCommandProvider> SourceGroupCxxCdb::getIndexerCommandProvider(const RefreshInfo& info) const
 {
 	std::shared_ptr<CxxIndexerCommandProvider> provider = std::make_shared<CxxIndexerCommandProvider>();
 
@@ -112,7 +112,7 @@ std::shared_ptr<IndexerCommandProvider> SourceGroupCxxCdb::getIndexerCommandProv
 			}
 		}
 
-		if (filesToIndex.find(sourcePath) != filesToIndex.end() &&
+		if (info.filesToIndex.find(sourcePath) != info.filesToIndex.end() &&
 			sourceFilePaths.find(sourcePath) != sourceFilePaths.end())
 		{
 			std::vector<std::wstring> cdbFlags = utility::convert<std::string, std::wstring>(
@@ -143,9 +143,9 @@ std::shared_ptr<IndexerCommandProvider> SourceGroupCxxCdb::getIndexerCommandProv
 	return provider;
 }
 
-std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCxxCdb::getIndexerCommands(const std::set<FilePath>& filesToIndex) const
+std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCxxCdb::getIndexerCommands(const RefreshInfo& info) const
 {
-	return getIndexerCommandProvider(filesToIndex)->consumeAllCommands();
+	return getIndexerCommandProvider(info)->consumeAllCommands();
 }
 
 std::shared_ptr<Task> SourceGroupCxxCdb::getPreIndexTask(
diff --git a/src/lib_cxx/project/SourceGroupCxxCdb.h b/src/lib_cxx/project/SourceGroupCxxCdb.h
index ce829c7e..7d9e2a5a 100644
--- a/src/lib_cxx/project/SourceGroupCxxCdb.h
+++ b/src/lib_cxx/project/SourceGroupCxxCdb.h
@@ -25,8 +25,8 @@ public:
 	std::set<FilePath> filterToContainedFilePaths(const std::set<FilePath>& filePaths) const override;
 	std::set<FilePath> getAllSourceFilePaths() const override;
 	std::set<FilePath> getAllSourceFilePaths(std::shared_ptr<clang::tooling::JSONCompilationDatabase> cdb) const;
-	std::shared_ptr<IndexerCommandProvider> getIndexerCommandProvider(const std::set<FilePath>& filesToIndex) const override;
-	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const std::set<FilePath>& filesToIndex) const override;
+	std::shared_ptr<IndexerCommandProvider> getIndexerCommandProvider(const RefreshInfo& info) const override;
+	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const RefreshInfo& info) const override;
 	std::shared_ptr<Task> getPreIndexTask(
 		std::shared_ptr<StorageProvider> storageProvider, std::shared_ptr<DialogView> dialogView) const override;
 
diff --git a/src/lib_cxx/project/SourceGroupCxxCodeblocks.cpp b/src/lib_cxx/project/SourceGroupCxxCodeblocks.cpp
index f20d8857..fe66583c 100644
--- a/src/lib_cxx/project/SourceGroupCxxCodeblocks.cpp
+++ b/src/lib_cxx/project/SourceGroupCxxCodeblocks.cpp
@@ -68,7 +68,7 @@ std::set<FilePath> SourceGroupCxxCodeblocks::getAllSourceFilePaths() const
 	return sourceFilePaths;
 }
 
-std::shared_ptr<IndexerCommandProvider> SourceGroupCxxCodeblocks::getIndexerCommandProvider(const std::set<FilePath>& filesToIndex) const
+std::shared_ptr<IndexerCommandProvider> SourceGroupCxxCodeblocks::getIndexerCommandProvider(const RefreshInfo& info) const
 {
 	std::shared_ptr<CxxIndexerCommandProvider> provider = std::make_shared<CxxIndexerCommandProvider>();
 
@@ -78,7 +78,7 @@ std::shared_ptr<IndexerCommandProvider> SourceGroupCxxCodeblocks::getIndexerComm
 	{
 		for (std::shared_ptr<IndexerCommandCxx> indexerCommand: project->getIndexerCommands(m_settings, ApplicationSettings::getInstance()))
 		{
-			if (filesToIndex.find(indexerCommand->getSourceFilePath()) != filesToIndex.end())
+			if (info.filesToIndex.find(indexerCommand->getSourceFilePath()) != info.filesToIndex.end())
 			{
 				provider->addCommand(indexerCommand);
 			}
@@ -87,9 +87,9 @@ std::shared_ptr<IndexerCommandProvider> SourceGroupCxxCodeblocks::getIndexerComm
 	return provider;
 }
 
-std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCxxCodeblocks::getIndexerCommands(const std::set<FilePath>& filesToIndex) const
+std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCxxCodeblocks::getIndexerCommands(const RefreshInfo& info) const
 {
-	return getIndexerCommandProvider(filesToIndex)->consumeAllCommands();
+	return getIndexerCommandProvider(info)->consumeAllCommands();
 }
 
 std::shared_ptr<SourceGroupSettings> SourceGroupCxxCodeblocks::getSourceGroupSettings()
diff --git a/src/lib_cxx/project/SourceGroupCxxCodeblocks.h b/src/lib_cxx/project/SourceGroupCxxCodeblocks.h
index 3acafeed..e8589d34 100644
--- a/src/lib_cxx/project/SourceGroupCxxCodeblocks.h
+++ b/src/lib_cxx/project/SourceGroupCxxCodeblocks.h
@@ -17,8 +17,8 @@ public:
 	bool prepareIndexing() override;
 	std::set<FilePath> filterToContainedFilePaths(const std::set<FilePath>& filePaths) const override;
 	std::set<FilePath> getAllSourceFilePaths() const override;
-	std::shared_ptr<IndexerCommandProvider> getIndexerCommandProvider(const std::set<FilePath>& filesToIndex) const override;
-	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const std::set<FilePath>& filesToIndex) const override;
+	std::shared_ptr<IndexerCommandProvider> getIndexerCommandProvider(const RefreshInfo& info) const override;
+	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const RefreshInfo& info) const override;
 
 private:
 	std::shared_ptr<SourceGroupSettings> getSourceGroupSettings() override;
diff --git a/src/lib_cxx/project/SourceGroupCxxEmpty.cpp b/src/lib_cxx/project/SourceGroupCxxEmpty.cpp
index d25f38e2..969aaa5d 100644
--- a/src/lib_cxx/project/SourceGroupCxxEmpty.cpp
+++ b/src/lib_cxx/project/SourceGroupCxxEmpty.cpp
@@ -5,6 +5,7 @@
 #include "FileManager.h"
 #include "IndexerCommandCxx.h"
 #include "logging.h"
+#include "RefreshInfo.h"
 #include "SourceGroupSettingsCEmpty.h"
 #include "SourceGroupSettingsCppEmpty.h"
 #include "SourceGroupSettingsWithCppStandard.h"
@@ -69,7 +70,7 @@ std::set<FilePath> SourceGroupCxxEmpty::getAllSourceFilePaths() const
 	return fileManager.getAllSourceFilePaths();
 }
 
-std::shared_ptr<IndexerCommandProvider> SourceGroupCxxEmpty::getIndexerCommandProvider(const std::set<FilePath>& filesToIndex) const
+std::shared_ptr<IndexerCommandProvider> SourceGroupCxxEmpty::getIndexerCommandProvider(const RefreshInfo& info) const
 {
 	std::set<FilePath> indexedPaths;
 	std::set<FilePathFilter> excludeFilters;
@@ -93,7 +94,7 @@ std::shared_ptr<IndexerCommandProvider> SourceGroupCxxEmpty::getIndexerCommandPr
 	std::shared_ptr<CxxIndexerCommandProvider> provider = std::make_shared<CxxIndexerCommandProvider>();
 	for (const FilePath& sourcePath: getAllSourceFilePaths())
 	{
-		if (filesToIndex.find(sourcePath) != filesToIndex.end())
+		if (info.filesToIndex.find(sourcePath) != info.filesToIndex.end())
 		{
 			provider->addCommand(std::make_shared<IndexerCommandCxx>(
 				sourcePath,
@@ -109,9 +110,9 @@ std::shared_ptr<IndexerCommandProvider> SourceGroupCxxEmpty::getIndexerCommandPr
 	return provider;
 }
 
-std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCxxEmpty::getIndexerCommands(const std::set<FilePath>& filesToIndex) const
+std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCxxEmpty::getIndexerCommands(const RefreshInfo& info) const
 {
-	return getIndexerCommandProvider(filesToIndex)->consumeAllCommands();
+	return getIndexerCommandProvider(info)->consumeAllCommands();
 }
 
 std::shared_ptr<Task> SourceGroupCxxEmpty::getPreIndexTask(
diff --git a/src/lib_cxx/project/SourceGroupCxxEmpty.h b/src/lib_cxx/project/SourceGroupCxxEmpty.h
index 45050b0f..2a0e6eee 100644
--- a/src/lib_cxx/project/SourceGroupCxxEmpty.h
+++ b/src/lib_cxx/project/SourceGroupCxxEmpty.h
@@ -16,8 +16,8 @@ public:
 
 	std::set<FilePath> filterToContainedFilePaths(const std::set<FilePath>& filePaths) const override;
 	std::set<FilePath> getAllSourceFilePaths() const override;
-	std::shared_ptr<IndexerCommandProvider> getIndexerCommandProvider(const std::set<FilePath>& filesToIndex) const override;
-	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const std::set<FilePath>& filesToIndex) const override;
+	std::shared_ptr<IndexerCommandProvider> getIndexerCommandProvider(const RefreshInfo& info) const override;
+	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const RefreshInfo& info) const override;
 	std::shared_ptr<Task> getPreIndexTask(
 		std::shared_ptr<StorageProvider> storageProvider, std::shared_ptr<DialogView> dialogView) const override;
 
diff --git a/src/lib_cxx/project/SourceGroupCxxSonargraph.cpp b/src/lib_cxx/project/SourceGroupCxxSonargraph.cpp
index 227c7b9f..920eec59 100644
--- a/src/lib_cxx/project/SourceGroupCxxSonargraph.cpp
+++ b/src/lib_cxx/project/SourceGroupCxxSonargraph.cpp
@@ -1,13 +1,13 @@
 #include "SourceGroupCxxSonargraph.h"
 
+#include "Application.h"
+#include "ApplicationSettings.h"
 #include "CxxIndexerCommandProvider.h"
 #include "IndexerCommandCxx.h"
-#include "ApplicationSettings.h"
-#include "SourceGroupSettingsCxxSonargraph.h"
 #include "MessageStatus.h"
+#include "SourceGroupSettingsCxxSonargraph.h"
 #include "SonargraphProject.h"
 #include "utility.h"
-#include "Application.h"
 
 SourceGroupCxxSonargraph::SourceGroupCxxSonargraph(std::shared_ptr<SourceGroupSettingsCxxSonargraph> settings)
 	: m_settings(settings)
@@ -55,7 +55,7 @@ std::set<FilePath> SourceGroupCxxSonargraph::getAllSourceFilePaths() const
 	return sourceFilePaths;
 }
 
-std::shared_ptr<IndexerCommandProvider> SourceGroupCxxSonargraph::getIndexerCommandProvider(const std::set<FilePath>& filesToIndex) const
+std::shared_ptr<IndexerCommandProvider> SourceGroupCxxSonargraph::getIndexerCommandProvider(const RefreshInfo& info) const
 {
 	std::shared_ptr<CxxIndexerCommandProvider> provider = std::make_shared<CxxIndexerCommandProvider>();
 	if (std::shared_ptr<Sonargraph::Project> project = Sonargraph::Project::load(
@@ -66,7 +66,7 @@ std::shared_ptr<IndexerCommandProvider> SourceGroupCxxSonargraph::getIndexerComm
 		{
 			if (std::shared_ptr<IndexerCommandCxx> indexerCommandCxx = std::dynamic_pointer_cast<IndexerCommandCxx>(indexerCommand))
 			{
-				if (filesToIndex.find(indexerCommand->getSourceFilePath()) != filesToIndex.end())
+				if (info.filesToIndex.find(indexerCommand->getSourceFilePath()) != info.filesToIndex.end())
 				{
 					provider->addCommand(indexerCommandCxx);
 				}
@@ -76,9 +76,9 @@ std::shared_ptr<IndexerCommandProvider> SourceGroupCxxSonargraph::getIndexerComm
 	return provider;
 }
 
-std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCxxSonargraph::getIndexerCommands(const std::set<FilePath>& filesToIndex) const
+std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCxxSonargraph::getIndexerCommands(const RefreshInfo& info) const
 {
-	return getIndexerCommandProvider(filesToIndex)->consumeAllCommands();
+	return getIndexerCommandProvider(info)->consumeAllCommands();
 }
 
 std::shared_ptr<SourceGroupSettings> SourceGroupCxxSonargraph::getSourceGroupSettings()
diff --git a/src/lib_cxx/project/SourceGroupCxxSonargraph.h b/src/lib_cxx/project/SourceGroupCxxSonargraph.h
index 99a12f47..fb7dcbe9 100644
--- a/src/lib_cxx/project/SourceGroupCxxSonargraph.h
+++ b/src/lib_cxx/project/SourceGroupCxxSonargraph.h
@@ -17,8 +17,8 @@ public:
 	bool prepareIndexing() override;
 	std::set<FilePath> filterToContainedFilePaths(const std::set<FilePath>& filePaths) const override;
 	std::set<FilePath> getAllSourceFilePaths() const override;
-	std::shared_ptr<IndexerCommandProvider> getIndexerCommandProvider(const std::set<FilePath>& filesToIndex) const override;
-	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const std::set<FilePath>& filesToIndex) const override;
+	std::shared_ptr<IndexerCommandProvider> getIndexerCommandProvider(const RefreshInfo& info) const override;
+	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const RefreshInfo& info) const override;
 
 private:
 	std::shared_ptr<SourceGroupSettings> getSourceGroupSettings() override;
diff --git a/src/lib_gui/qt/project_wizard/content/QtProjectWizardContentPreferences.cpp b/src/lib_gui/qt/project_wizard/content/QtProjectWizardContentPreferences.cpp
index cc5b5745..97f62935 100644
--- a/src/lib_gui/qt/project_wizard/content/QtProjectWizardContentPreferences.cpp
+++ b/src/lib_gui/qt/project_wizard/content/QtProjectWizardContentPreferences.cpp
@@ -372,7 +372,7 @@ void QtProjectWizardContentPreferences::populate(QGridLayout* layout, int& row)
 	addTitle("Python", layout, row);
 
 	m_pythonPostProcessing = addCheckBox("Post Processing",
-		"Add ambiguous edges for unsolved references",
+		"Add ambiguous edges for unsolved references (recommended)",
 		"<p>Enable a post processing step to solve unsolved references after the indexing is done. </p>"
 		"<p>These references will be marked \"ambiguous\" to indicate that some of these edges may never "
 		"be encountered during runtime of the indexed code because the post processing only relies on "
diff --git a/src/lib_gui/qt/view/QtDialogView.cpp b/src/lib_gui/qt/view/QtDialogView.cpp
index 30cf7232..dd76849a 100644
--- a/src/lib_gui/qt/view/QtDialogView.cpp
+++ b/src/lib_gui/qt/view/QtDialogView.cpp
@@ -138,10 +138,11 @@ void QtDialogView::hideProgressDialog()
 }
 
 void QtDialogView::startIndexingDialog(
-	Project* project, const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode,
+	Project* project, const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode, bool enabledShallowOption, bool initialShallowState,
 	std::function<void(const RefreshInfo& info)> onStartIndexing, std::function<void()> onCancelIndexing)
 {
 	m_refreshInfos.clear();
+	m_shallowIndexingEnabled = initialShallowState;
 
 	m_onQtThread(
 		[=]()
@@ -149,7 +150,14 @@ void QtDialogView::startIndexingDialog(
 			m_dialogsVisible = true;
 			m_windowStack.clearWindows();
 
-			QtIndexingStartDialog* window = createWindow<QtIndexingStartDialog>(enabledModes, initialMode);
+			QtIndexingStartDialog* window = createWindow<QtIndexingStartDialog>(enabledModes, initialMode, enabledShallowOption, initialShallowState);
+
+			connect(window, &QtIndexingStartDialog::setShallowIndexing,
+				[=](bool enabled)
+				{
+					m_shallowIndexingEnabled = enabled;
+				}
+			);
 
 			std::function<void(RefreshMode)> onRefreshModeChanged = (
 				[=](RefreshMode refreshMode)
@@ -200,6 +208,7 @@ void QtDialogView::startIndexingDialog(
 				[=](RefreshMode refreshMode)
 				{
 					RefreshInfo info = m_refreshInfos.find(refreshMode)->second;
+					info.shallow = m_shallowIndexingEnabled;
 					Task::dispatch(TabId::app(), std::make_shared<TaskLambda>(
 						[=]()
 						{
@@ -288,7 +297,7 @@ void QtDialogView::updateCustomIndexingDialog(
 
 DatabasePolicy QtDialogView::finishedIndexingDialog(
 	size_t indexedFileCount, size_t totalIndexedFileCount, size_t completedFileCount, size_t totalFileCount,
-	float time, ErrorCountInfo errorInfo, bool interrupted)
+	float time, ErrorCountInfo errorInfo, bool interrupted, bool shallow)
 {
 	DatabasePolicy policy = DATABASE_POLICY_UNKNOWN;
 	m_resultReady = false;
@@ -299,7 +308,7 @@ DatabasePolicy QtDialogView::finishedIndexingDialog(
 			m_dialogsVisible = true;
 			m_windowStack.clearWindows();
 
-			QtIndexingReportDialog* window = createWindow<QtIndexingReportDialog>(indexedFileCount, totalIndexedFileCount, completedFileCount, totalFileCount, time, interrupted);
+			QtIndexingReportDialog* window = createWindow<QtIndexingReportDialog>(indexedFileCount, totalIndexedFileCount, completedFileCount, totalFileCount, time, interrupted, shallow);
 			window->updateErrorCount(errorInfo.total, errorInfo.fatal);
 			connect(window, &QtIndexingDialog::finished,
 				[this, &policy]()
@@ -317,6 +326,14 @@ DatabasePolicy QtDialogView::finishedIndexingDialog(
 					m_resultReady = true;
 				}
 			);
+			connect(window, &QtIndexingReportDialog::requestReindexing,
+				[this, &policy]()
+				{
+					setUIBlocked(false);
+					policy = DATABASE_POLICY_REFRESH;
+					m_resultReady = true;
+				}
+			);
 
 			m_mainWindow->hideWindowsTaskbarProgress();
 			setUIBlocked(true);
diff --git a/src/lib_gui/qt/view/QtDialogView.h b/src/lib_gui/qt/view/QtDialogView.h
index 34a8643f..8a8502ca 100644
--- a/src/lib_gui/qt/view/QtDialogView.h
+++ b/src/lib_gui/qt/view/QtDialogView.h
@@ -37,7 +37,7 @@ public:
 	void hideProgressDialog() override;
 
 	void startIndexingDialog(
-		Project* project, const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode,
+		Project* project, const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode, bool enabledShallowOption, bool initialShallowState,
 		std::function<void(const RefreshInfo& info)> onStartIndexing, std::function<void()> onCancelIndexing) override;
 	void updateIndexingDialog(
 		size_t startedFileCount, size_t finishedFileCount, size_t totalFileCount, const std::vector<FilePath>& sourcePaths) override;
@@ -45,7 +45,7 @@ public:
 		size_t startedFileCount, size_t finishedFileCount, size_t totalFileCount, const std::vector<FilePath>& sourcePaths) override;
 	DatabasePolicy finishedIndexingDialog(
 		size_t indexedFileCount, size_t totalIndexedFileCount, size_t completedFileCount, size_t totalFileCount,
-		float time, ErrorCountInfo errorInfo, bool interrupted) override;
+		float time, ErrorCountInfo errorInfo, bool interrupted, bool shallow) override;
 
 	int confirm(const std::wstring& message, const std::vector<std::wstring>& options) override;
 
@@ -78,6 +78,7 @@ private:
 	QtThreadedLambdaFunctor m_onQtThread3;
 
 	std::map<RefreshMode, RefreshInfo> m_refreshInfos;
+	bool m_shallowIndexingEnabled;
 
 	bool m_resultReady;
 	bool m_uiBlocked = false;
diff --git a/src/lib_gui/qt/window/QtIndexingReportDialog.cpp b/src/lib_gui/qt/window/QtIndexingReportDialog.cpp
index fa03c95e..8acee891 100644
--- a/src/lib_gui/qt/window/QtIndexingReportDialog.cpp
+++ b/src/lib_gui/qt/window/QtIndexingReportDialog.cpp
@@ -4,10 +4,12 @@
 #include <QPushButton>
 
 #include "MessageErrorsHelpMessage.h"
+#include "MessageIndexingShowDialog.h"
+#include "MessageRefresh.h"
 #include "TimeStamp.h"
 
 QtIndexingReportDialog::QtIndexingReportDialog(
-	size_t indexedFileCount, size_t totalIndexedFileCount, size_t completedFileCount, size_t totalFileCount, float time, bool interrupted, QWidget* parent)
+	size_t indexedFileCount, size_t totalIndexedFileCount, size_t completedFileCount, size_t totalFileCount, float time, bool interrupted, bool shallow, QWidget* parent)
 	: QtIndexingDialog(true, parent)
 	, m_interrupted(interrupted)
 {
@@ -17,6 +19,10 @@ QtIndexingReportDialog::QtIndexingReportDialog(
 	{
 		QtIndexingDialog::createTitleLabel("Interrupted Indexing", m_layout);
 	}
+	else if (shallow)
+	{
+		QtIndexingDialog::createTitleLabel("Finished Shallow Indexing", m_layout);
+	}
 	else
 	{
 		QtIndexingDialog::createTitleLabel("Finished Indexing", m_layout);
@@ -40,6 +46,14 @@ QtIndexingReportDialog::QtIndexingReportDialog(
 
 	m_layout->addStretch();
 
+	if (shallow)
+	{
+		createMessageLabel(m_layout)->setText(
+			"<i>You can now browse your project while running a second pass for in-depth indexing!</i>"
+		);
+		m_layout->addSpacing(12);
+	}
+
 	{
 		QHBoxLayout* buttons = new QHBoxLayout();
 		if (interrupted)
@@ -49,10 +63,17 @@ QtIndexingReportDialog::QtIndexingReportDialog(
 			connect(discardButton, &QPushButton::clicked, this, &QtIndexingReportDialog::onDiscardPressed);
 			buttons->addWidget(discardButton);
 		}
+		else if (shallow)
+		{
+			QPushButton* startInDepthButton = new QPushButton("Start In-Depth Indexing");
+			startInDepthButton->setObjectName("windowButton");
+			connect(startInDepthButton, &QPushButton::clicked, this, &QtIndexingReportDialog::onStartInDepthPressed);
+			buttons->addWidget(startInDepthButton);
+		}
 
 		buttons->addStretch();
 
-		QPushButton* confirmButton = new QPushButton(interrupted ? "Keep" : "OK");
+		QPushButton* confirmButton = new QPushButton(interrupted ? "Keep" : (shallow ? "Quit" : "OK"));
 		confirmButton->setObjectName("windowButton");
 		confirmButton->setDefault(true);
 		connect(confirmButton, &QPushButton::clicked, this, &QtIndexingReportDialog::onConfirmPressed);
@@ -128,3 +149,8 @@ void QtIndexingReportDialog::onDiscardPressed()
 {
 	emit QtIndexingDialog::canceled();
 }
+
+void QtIndexingReportDialog::onStartInDepthPressed()
+{
+	emit requestReindexing();
+}
diff --git a/src/lib_gui/qt/window/QtIndexingReportDialog.h b/src/lib_gui/qt/window/QtIndexingReportDialog.h
index 34455b6f..14e437af 100644
--- a/src/lib_gui/qt/window/QtIndexingReportDialog.h
+++ b/src/lib_gui/qt/window/QtIndexingReportDialog.h
@@ -8,8 +8,11 @@ class QtIndexingReportDialog
 {
 	Q_OBJECT
 
+signals :
+	void requestReindexing();
+
 public:
-	QtIndexingReportDialog(size_t indexedFileCount, size_t totalIndexedFileCount, size_t completedFileCount, size_t totalFileCount, float time, bool interrupted, QWidget* parent = 0);
+	QtIndexingReportDialog(size_t indexedFileCount, size_t totalIndexedFileCount, size_t completedFileCount, size_t totalFileCount, float time, bool interrupted, bool shallow, QWidget* parent = 0);
 	QSize sizeHint() const override;
 
 	void updateErrorCount(size_t errorCount, size_t fatalCount);
@@ -21,6 +24,7 @@ protected:
 private:
 	void onConfirmPressed();
 	void onDiscardPressed();
+	void onStartInDepthPressed();
 
 	QWidget* m_errorWidget;
 	bool m_interrupted;
diff --git a/src/lib_gui/qt/window/QtIndexingStartDialog.cpp b/src/lib_gui/qt/window/QtIndexingStartDialog.cpp
index 08ebf630..3e1bf757 100644
--- a/src/lib_gui/qt/window/QtIndexingStartDialog.cpp
+++ b/src/lib_gui/qt/window/QtIndexingStartDialog.cpp
@@ -1,12 +1,13 @@
 #include "QtIndexingStartDialog.h"
 
+#include <QCheckBox>
 #include <QLabel>
-#include <QRadioButton>
 #include <QPushButton>
+#include <QRadioButton>
 
 #include "QtHelpButton.h"
 
-QtIndexingStartDialog::QtIndexingStartDialog(const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode, QWidget* parent)
+QtIndexingStartDialog::QtIndexingStartDialog(const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode, bool enabledShallowOption, bool initialShallowState, QWidget* parent)
 	: QtIndexingDialog(true, parent)
 {
 	setSizeGripStyle(false);
@@ -37,11 +38,18 @@ QtIndexingStartDialog::QtIndexingStartDialog(const std::vector<RefreshMode>& ena
 
 	QtHelpButton* helpButton = new QtHelpButton(
 		"Indexing Modes",
-		"<b>Updated files:</b> Reindexes all files that were modified since the last indexing, all files depending "
-		"on those and new files.<br /><br />"
-		"<b>Incomplete & updated files:</b> Reindexes all files that had errors during last indexing, all files "
-		"depending on those and all updated files.<br /><br />"
-		"<b>All files:</b> Deletes the previous index and reindexes all files.<br /><br />"
+		QString("<b>Updated files:</b> Reindexes all files that were modified since the last indexing, all new files and all files depending "
+			"on those.<br /><br />"
+			"<b>Incomplete & updated files:</b> Reindexes all files that had errors during last indexing, all updated files and all files "
+			"depending on those.<br /><br />"
+			"<b>All files:</b> Deletes the previous index and reindexes all files from scratch.<br /><br />") +
+			(enabledShallowOption ?
+				"<br /><b>Shallow Python Indexing:</b> References within your code base (calls, usages, etc.) are resolved by name, which is "
+				"imprecise but much faster than in-depth indexing.<br />"
+				"<i>Hint: Use this option for a quick first indexing pass and start browsing the code base "
+				"while running a second pass for in-depth indexing.<br /><br />" :
+				""
+			)
 	);
 	helpButton->setColor(Qt::white);
 	modeTitleLayout->addWidget(helpButton);
@@ -91,6 +99,14 @@ QtIndexingStartDialog::QtIndexingStartDialog(const std::vector<RefreshMode>& ena
 		m_refreshModeButtons[mode]->setEnabled(true);
 	}
 
+	if (enabledShallowOption)
+	{
+		QCheckBox* shallowIndexingCheckBox = new QCheckBox("Shallow Python Indexing");
+		connect(shallowIndexingCheckBox, &QCheckBox::toggled, [=]() { emit setShallowIndexing(shallowIndexingCheckBox->isChecked()); });
+		shallowIndexingCheckBox->setChecked(initialShallowState);
+		modeLayout->addWidget(shallowIndexingCheckBox);
+	}
+
 	subLayout->addLayout(modeLayout);
 	m_layout->addLayout(subLayout);
 
diff --git a/src/lib_gui/qt/window/QtIndexingStartDialog.h b/src/lib_gui/qt/window/QtIndexingStartDialog.h
index 0aaad08c..e81505a5 100644
--- a/src/lib_gui/qt/window/QtIndexingStartDialog.h
+++ b/src/lib_gui/qt/window/QtIndexingStartDialog.h
@@ -14,10 +14,11 @@ class QtIndexingStartDialog
 
 signals:
 	void setMode(RefreshMode mode);
+	void setShallowIndexing(bool enabled);
 	void startIndexing(RefreshMode mode);
 
 public:
-	QtIndexingStartDialog(const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode, QWidget* parent = 0);
+	QtIndexingStartDialog(const std::vector<RefreshMode>& enabledModes, const RefreshMode initialMode, bool enabledShallowOption, bool initialShallowState, QWidget* parent = 0);
 	QSize sizeHint() const override;
 
 	void updateRefreshInfo(const RefreshInfo& info);
diff --git a/src/lib_java/project/SourceGroupJava.cpp b/src/lib_java/project/SourceGroupJava.cpp
index ff60d95a..de51384b 100644
--- a/src/lib_java/project/SourceGroupJava.cpp
+++ b/src/lib_java/project/SourceGroupJava.cpp
@@ -3,6 +3,7 @@
 #include "IndexerCommandJava.h"
 #include "FileManager.h"
 #include "logging.h"
+#include "RefreshInfo.h"
 #include "SourceGroupSettings.h"
 #include "SourceGroupSettingsWithExcludeFilters.h"
 #include "SourceGroupSettingsWithJavaStandard.h"
@@ -33,7 +34,7 @@ std::set<FilePath> SourceGroupJava::getAllSourceFilePaths() const
 	return fileManager.getAllSourceFilePaths();
 }
 
-std::vector<std::shared_ptr<IndexerCommand>> SourceGroupJava::getIndexerCommands(const std::set<FilePath>& filesToIndex) const
+std::vector<std::shared_ptr<IndexerCommand>> SourceGroupJava::getIndexerCommands(const RefreshInfo& info) const
 {
 	const std::wstring languageStandard =
 		dynamic_cast<const SourceGroupSettingsWithJavaStandard*>(getSourceGroupSettings().get())->getJavaStandard();
@@ -43,7 +44,7 @@ std::vector<std::shared_ptr<IndexerCommand>> SourceGroupJava::getIndexerCommands
 	std::vector<std::shared_ptr<IndexerCommand>> indexerCommands;
 	for (const FilePath& sourcePath: getAllSourceFilePaths())
 	{
-		if (filesToIndex.find(sourcePath) != filesToIndex.end())
+		if (info.filesToIndex.find(sourcePath) != info.filesToIndex.end())
 		{
 			indexerCommands.push_back(std::make_shared<IndexerCommandJava>(
 				sourcePath, languageStandard, classPath
diff --git a/src/lib_java/project/SourceGroupJava.h b/src/lib_java/project/SourceGroupJava.h
index 9419a846..8fef4c47 100644
--- a/src/lib_java/project/SourceGroupJava.h
+++ b/src/lib_java/project/SourceGroupJava.h
@@ -13,7 +13,7 @@ class SourceGroupJava
 public:
 	std::set<FilePath> filterToContainedFilePaths(const std::set<FilePath>& filePaths) const override;
 	std::set<FilePath> getAllSourceFilePaths() const override;
-	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const std::set<FilePath>& filesToIndex) const override;
+	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const RefreshInfo& info) const override;
 
 private:
 	virtual std::vector<FilePath> getAllSourcePaths() const = 0;
diff --git a/src/lib_java/project/SourceGroupJavaSonargraph.cpp b/src/lib_java/project/SourceGroupJavaSonargraph.cpp
index bc04c87d..464d0304 100644
--- a/src/lib_java/project/SourceGroupJavaSonargraph.cpp
+++ b/src/lib_java/project/SourceGroupJavaSonargraph.cpp
@@ -1,12 +1,13 @@
 #include "SourceGroupJavaSonargraph.h"
 
-#include "IndexerCommandJava.h"
-#include "ApplicationSettings.h"
-#include "SourceGroupSettingsJavaSonargraph.h"
-#include "MessageStatus.h"
-#include "SonargraphProject.h"
-#include "utilityJava.h"
 #include "Application.h"
+#include "ApplicationSettings.h"
+#include "IndexerCommandJava.h"
+#include "MessageStatus.h"
+#include "RefreshInfo.h"
+#include "SonargraphProject.h"
+#include "SourceGroupSettingsJavaSonargraph.h"
+#include "utilityJava.h"
 
 SourceGroupJavaSonargraph::SourceGroupJavaSonargraph(std::shared_ptr<SourceGroupSettingsJavaSonargraph> settings)
 	: m_settings(settings)
@@ -65,7 +66,7 @@ std::set<FilePath> SourceGroupJavaSonargraph::getAllSourceFilePaths() const
 	return std::set<FilePath>();
 }
 
-std::vector<std::shared_ptr<IndexerCommand>> SourceGroupJavaSonargraph::getIndexerCommands(const std::set<FilePath>& filesToIndex) const
+std::vector<std::shared_ptr<IndexerCommand>> SourceGroupJavaSonargraph::getIndexerCommands(const RefreshInfo& info) const
 {
 	std::vector<std::shared_ptr<IndexerCommand>> indexerCommands;
 
@@ -75,7 +76,7 @@ std::vector<std::shared_ptr<IndexerCommand>> SourceGroupJavaSonargraph::getIndex
 	{
 		for (std::shared_ptr<IndexerCommand> indexerCommand : project->getIndexerCommands(m_settings, ApplicationSettings::getInstance()))
 		{
-			if (filesToIndex.find(indexerCommand->getSourceFilePath()) != filesToIndex.end())
+			if (info.filesToIndex.find(indexerCommand->getSourceFilePath()) != info.filesToIndex.end())
 			{
 				indexerCommands.push_back(indexerCommand);
 			}
diff --git a/src/lib_java/project/SourceGroupJavaSonargraph.h b/src/lib_java/project/SourceGroupJavaSonargraph.h
index c0584ad7..d92c2cbb 100644
--- a/src/lib_java/project/SourceGroupJavaSonargraph.h
+++ b/src/lib_java/project/SourceGroupJavaSonargraph.h
@@ -17,7 +17,7 @@ public:
 	bool prepareIndexing() override;
 	std::set<FilePath> filterToContainedFilePaths(const std::set<FilePath>& filePaths) const override;
 	std::set<FilePath> getAllSourceFilePaths() const override;
-	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const std::set<FilePath>& filesToIndex) const override;
+	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const RefreshInfo& info) const override;
 
 private:
 	std::shared_ptr<SourceGroupSettings> getSourceGroupSettings() override;
diff --git a/src/lib_python/project/SourceGroupPythonEmpty.cpp b/src/lib_python/project/SourceGroupPythonEmpty.cpp
index 6403c420..e5bd7fac 100644
--- a/src/lib_python/project/SourceGroupPythonEmpty.cpp
+++ b/src/lib_python/project/SourceGroupPythonEmpty.cpp
@@ -4,6 +4,7 @@
 #include "FileManager.h"
 #include "IndexerCommandCustom.h"
 #include "ProjectSettings.h"
+#include "RefreshInfo.h"
 #include "ResourcePaths.h"
 #include "SourceGroupSettingsPythonEmpty.h"
 #include "SqliteIndexStorage.h"
@@ -19,6 +20,12 @@ bool SourceGroupPythonEmpty::allowsPartialClearing() const
 	return false;
 }
 
+bool SourceGroupPythonEmpty::allowsShallowIndexing() const
+{
+	return true;
+}
+
+
 std::set<FilePath> SourceGroupPythonEmpty::filterToContainedFilePaths(const std::set<FilePath>& filePaths) const
 {
 	return SourceGroup::filterToContainedFilePaths(
@@ -40,7 +47,7 @@ std::set<FilePath> SourceGroupPythonEmpty::getAllSourceFilePaths() const
 	return fileManager.getAllSourceFilePaths();
 }
 
-std::vector<std::shared_ptr<IndexerCommand>> SourceGroupPythonEmpty::getIndexerCommands(const std::set<FilePath>& filesToIndex) const
+std::vector<std::shared_ptr<IndexerCommand>> SourceGroupPythonEmpty::getIndexerCommands(const RefreshInfo& info) const
 {
 	std::wstring args = L"";
 
@@ -57,10 +64,15 @@ std::vector<std::shared_ptr<IndexerCommand>> SourceGroupPythonEmpty::getIndexerC
 		args += L" --verbose";
 	}
 
+	if (info.shallow)
+	{
+		args += L" --shallow";
+	}
+
 	std::vector<std::shared_ptr<IndexerCommand>> indexerCommands;
 	for (const FilePath& sourceFilePath : getAllSourceFilePaths())
 	{
-		if (filesToIndex.find(sourceFilePath) != filesToIndex.end())
+		if (info.filesToIndex.find(sourceFilePath) != info.filesToIndex.end())
 		{
 			indexerCommands.push_back(std::make_shared<IndexerCommandCustom>(
 				INDEXER_COMMAND_PYTHON,
diff --git a/src/lib_python/project/SourceGroupPythonEmpty.h b/src/lib_python/project/SourceGroupPythonEmpty.h
index a14fe8ea..5d38f9c3 100644
--- a/src/lib_python/project/SourceGroupPythonEmpty.h
+++ b/src/lib_python/project/SourceGroupPythonEmpty.h
@@ -14,9 +14,10 @@ public:
 	SourceGroupPythonEmpty(std::shared_ptr<SourceGroupSettingsPythonEmpty> settings);
 
 	bool allowsPartialClearing() const override;
+	bool allowsShallowIndexing() const override;
 	std::set<FilePath> filterToContainedFilePaths(const std::set<FilePath>& filePaths) const override;
 	std::set<FilePath> getAllSourceFilePaths() const override;
-	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const std::set<FilePath>& filesToIndex) const override;
+	std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const RefreshInfo& info) const override;
 
 private:
 	std::shared_ptr<SourceGroupSettings> getSourceGroupSettings() override;
diff --git a/src/test/RefreshInfoGeneratorTestSuite.cpp b/src/test/RefreshInfoGeneratorTestSuite.cpp
index b4b8e138..d6accd0a 100644
--- a/src/test/RefreshInfoGeneratorTestSuite.cpp
+++ b/src/test/RefreshInfoGeneratorTestSuite.cpp
@@ -80,7 +80,7 @@ namespace
 			return m_sourceFilePaths;
 		}
 
-		std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const std::set<FilePath>& filesToIndex) const override
+		std::vector<std::shared_ptr<IndexerCommand>> getIndexerCommands(const RefreshInfo& info) const override
 		{
 			return std::vector<std::shared_ptr<IndexerCommand>>();
 		}
diff --git a/src/test/SourceGroupTestSuite.cpp b/src/test/SourceGroupTestSuite.cpp
index b310d62e..d065569e 100644
--- a/src/test/SourceGroupTestSuite.cpp
+++ b/src/test/SourceGroupTestSuite.cpp
@@ -157,7 +157,9 @@ namespace
 	{
 		const FilePath projectDataRoot = getInputDirectoryPath(projectName).makeAbsolute();
 
-		std::vector<std::shared_ptr<IndexerCommand>> indexerCommands = sourceGroup->getIndexerCommands(sourceGroup->getAllSourceFilePaths());
+		RefreshInfo info;
+		info.filesToIndex = sourceGroup->getAllSourceFilePaths();
+		std::vector<std::shared_ptr<IndexerCommand>> indexerCommands = sourceGroup->getIndexerCommands(info);
 
 		std::sort(
 			indexerCommands.begin(),