because the timestamp has changed. Getting a smudged file can also
cause this. Avoid this by preserving timestamp of smudged files
when manipulating.
+* Clean filter should check if the filename was already in use by an old
+ key. The annex object for it may have been modified due to hard link, and
+ that should be cleaned up when the new version is added.
* Reconcile staged changes into the associated files database, whenever
the database is queried.
* See if the cases where the Keys database is not used can be