By mistake we've added following lines in our magnolia.properties since those needed modification while upgrading to 4.4.1:

magnolia.cache.startdir=${magnolia.app.rootdir}/cache
magnolia.repositories.home=${magnolia.app.rootdir}/repositories

Theoretically those lines look ok but at the end they have a whitespace. It resulted in Magnolia creating such directories on next start and we ended up with 'repositories', 'repositories ', 'cache' and 'cache ' in our directory structure. This was probably a killer for our upgrade that happened just after this properties edition. So, it could be useful to trim such properties as those can potentially lead to data inconsistency between db and repositories for example.