logic: record and display include edges for non-indexed files

* non-indexed files are shown in graph view and in code view
* non-indexed files are ignored in search view, overview, stats and refresh dialog

src/lib/project/RefreshInfo.h

@@ -17,6 +17,8 @@ struct RefreshInfo
 {
 	std::set<FilePath> filesToIndex;
 	std::set<FilePath> filesToClear;
+	std::set<FilePath> nonIndexedFilesToClear;
+
 	RefreshMode mode = REFRESH_NONE;
 };