See http://www.docear.org/support/forums/docear-support-forums-group3/bug-reports-forum6/searching-orphaned-annotations-is-taking-ages-thread1412.0/#postid-5031.
Performance bug identified in MonitoringWorker.searchingOrphanedNodes.

It loops over all annotations. For each annotation A it checks if A is still present in its file F.
This means that if F has 100 annotations, it is opened 100 times during searchingOrphanedNodes.
The loop should be "switched around" so that F is only opened once.