diff --git a/bin/app/data/gui/icon/sonargraph_icon.png b/bin/app/data/gui/icon/sonargraph_icon.png
index 571f1149..9100eb4f 100644
Binary files a/bin/app/data/gui/icon/sonargraph_icon.png and b/bin/app/data/gui/icon/sonargraph_icon.png differ
diff --git a/src/lib/data/indexer/IndexerCommandList.cpp b/src/lib/data/indexer/IndexerCommandList.cpp
index fbfe0024..a66984b3 100644
--- a/src/lib/data/indexer/IndexerCommandList.cpp
+++ b/src/lib/data/indexer/IndexerCommandList.cpp
@@ -35,7 +35,14 @@ void IndexerCommandList::shuffle()
 	std::vector<PairType> sourceFileSizesToCommands;
 	for (std::shared_ptr<IndexerCommand> command: m_commands)
 	{
-		sourceFileSizesToCommands.push_back(std::make_pair(FileSystem::getFileByteSize(command->getSourceFilePath()), command));
+		if (command->getSourceFilePath().exists())
+		{
+			sourceFileSizesToCommands.push_back(std::make_pair(FileSystem::getFileByteSize(command->getSourceFilePath()), command));
+		}
+		else
+		{
+			sourceFileSizesToCommands.push_back(std::make_pair(1, command));
+		}
 	}
 	std::sort(sourceFileSizesToCommands.begin(), sourceFileSizesToCommands.end(), [](const PairType& p, const PairType& q){ return p.first > q.first; });
 
diff --git a/src/lib/project/RefreshInfoGenerator.cpp b/src/lib/project/RefreshInfoGenerator.cpp
index b45e168f..f952e79e 100644
--- a/src/lib/project/RefreshInfoGenerator.cpp
+++ b/src/lib/project/RefreshInfoGenerator.cpp
@@ -170,7 +170,13 @@ std::set<FilePath> RefreshInfoGenerator::getAllSourceFilePaths(const std::vector
 	{
 		if (sourceGroup->getStatus() == SOURCE_GROUP_STATUS_ENABLED)
 		{
-			utility::append(allSourceFilePaths, sourceGroup->getAllSourceFilePaths());
+			for (const FilePath& sourceFilePath : sourceGroup->getAllSourceFilePaths())
+			{
+				if (sourceFilePath.exists())
+				{
+					allSourceFilePaths.insert(sourceFilePath);
+				}
+			}
 		}
 	}
 
diff --git a/src/lib_cxx/project/SourceGroupCxxSonargraph.cpp b/src/lib_cxx/project/SourceGroupCxxSonargraph.cpp
index a2c1f41b..aad71442 100644
--- a/src/lib_cxx/project/SourceGroupCxxSonargraph.cpp
+++ b/src/lib_cxx/project/SourceGroupCxxSonargraph.cpp
@@ -1,5 +1,6 @@
 #include "project/SourceGroupCxxSonargraph.h"
 
+#include "data/indexer/IndexerCommand.h"
 #include "settings/ApplicationSettings.h"
 #include "settings/SourceGroupSettingsCxxSonargraph.h"
 #include "utility/messaging/type/MessageStatus.h"
@@ -66,7 +67,13 @@ std::vector<std::shared_ptr<IndexerCommand>> SourceGroupCxxSonargraph::getIndexe
 		m_settings->getSonargraphProjectPathExpandedAndAbsolute(), getLanguage()
 	))
 	{
-		indexerCommands = project->getIndexerCommands(m_settings, ApplicationSettings::getInstance());
+		for (std::shared_ptr<IndexerCommand> indexerCommand : project->getIndexerCommands(m_settings, ApplicationSettings::getInstance()))
+		{
+			if (filesToIndex.find(indexerCommand->getSourceFilePath()) != filesToIndex.end())
+			{
+				indexerCommands.push_back(indexerCommand);
+			}
+		}
 	}
 	return indexerCommands;
 }
diff --git a/src/lib_java/project/SourceGroupJavaSonargraph.cpp b/src/lib_java/project/SourceGroupJavaSonargraph.cpp
index a83d628f..860a0e1a 100644
--- a/src/lib_java/project/SourceGroupJavaSonargraph.cpp
+++ b/src/lib_java/project/SourceGroupJavaSonargraph.cpp
@@ -75,7 +75,13 @@ std::vector<std::shared_ptr<IndexerCommand>> SourceGroupJavaSonargraph::getIndex
 		m_settings->getSonargraphProjectPathExpandedAndAbsolute(), getLanguage()
 	))
 	{
-		indexerCommands = project->getIndexerCommands(m_settings, ApplicationSettings::getInstance());
+		for (std::shared_ptr<IndexerCommand> indexerCommand : project->getIndexerCommands(m_settings, ApplicationSettings::getInstance()))
+		{
+			if (filesToIndex.find(indexerCommand->getSourceFilePath()) != filesToIndex.end())
+			{
+				indexerCommands.push_back(indexerCommand);
+			}
+		}
 	}
 
 	if (!indexerCommands.empty())
diff --git a/src/test/RefreshInfoGeneratorTestSuite.h b/src/test/RefreshInfoGeneratorTestSuite.h
index cf88ecee..712c649d 100644
--- a/src/test/RefreshInfoGeneratorTestSuite.h
+++ b/src/test/RefreshInfoGeneratorTestSuite.h
@@ -31,21 +31,27 @@ public:
 
 	void test_refresh_info_for_all_files_has_nothing_to_clear_and_specified_source_files_for_basic_sourcegroup()
 	{
-		const FilePath sourceFilePath = m_sourceFolder.getConcatenated(L"main.cpp");
+		cleanup();
+		{
+			const FilePath sourceFilePath = m_sourceFolder.getConcatenated(L"main.cpp");
 
-		std::vector<std::shared_ptr<SourceGroup>> sourceGroups;
-		sourceGroups.push_back(std::shared_ptr<SourceGroupTest>(new SourceGroupTest({ sourceFilePath })));
+			std::vector<std::shared_ptr<SourceGroup>> sourceGroups;
+			sourceGroups.push_back(std::shared_ptr<SourceGroupTest>(new SourceGroupTest({ sourceFilePath })));
 
-		const RefreshInfo refreshInfo = RefreshInfoGenerator::getRefreshInfoForAllFiles(sourceGroups);
+			addFileToFileSystem(sourceFilePath);
 
-		TS_ASSERT_EQUALS(REFRESH_ALL_FILES, refreshInfo.mode);
-		TS_ASSERT_EQUALS(0, refreshInfo.nonIndexedFilesToClear.size());
-		TS_ASSERT_EQUALS(0, refreshInfo.filesToClear.size());
-		TS_ASSERT_EQUALS(1, refreshInfo.filesToIndex.size());
+			const RefreshInfo refreshInfo = RefreshInfoGenerator::getRefreshInfoForAllFiles(sourceGroups);
 
-		TS_ASSERT(utility::containsElement<FilePath>(
-			utility::toVector(refreshInfo.filesToIndex), sourceFilePath
-		));
+			TS_ASSERT_EQUALS(REFRESH_ALL_FILES, refreshInfo.mode);
+			TS_ASSERT_EQUALS(0, refreshInfo.nonIndexedFilesToClear.size());
+			TS_ASSERT_EQUALS(0, refreshInfo.filesToClear.size());
+			TS_ASSERT_EQUALS(1, refreshInfo.filesToIndex.size());
+
+			TS_ASSERT(utility::containsElement<FilePath>(
+				utility::toVector(refreshInfo.filesToIndex), sourceFilePath
+				));
+		}
+		cleanup();
 	}
 
 	void test_refresh_info_for_updated_files_is_empty_for_empty_storage_and_empty_sourcegroup()