Deleting files from repository in filesystem confuses Archiva

Archiva seems to have a problem when files and/or directories from its repository are deleted.

I see lots of exceptions and such messages in the archiva.log:

2016-09-22 17:08:02,435 [pool-6-thread-1] ERROR
org.apache.jackrabbit.core.persistence.bundle.BundleFsPersistenceManager
[] - failed to read bundle: b9706fc7-846b-4dab-bac3-7a734136dbf8:
java.io.EOFException
2016-09-22 17:08:02,477 [pool-6-thread-1] ERROR
org.apache.jackrabbit.core.persistence.bundle.BundleFsPersistenceManager
[] - failed to read bundle: b9706fc7-846b-4dab-bac3-7a734136dbf8:
java.io.EOFException
2016-09-22 17:08:02,528 [pool-6-thread-1] ERROR
org.apache.jackrabbit.core.persistence.bundle.BundleFsPersistenceManager
[] - failed to read bundle: b9706fc7-846b-4dab-bac3-7a734136dbf8:
java.io.EOFException
2016-09-22 17:08:02,549 [pool-6-thread-1] ERROR
org.apache.jackrabbit.core.persistence.bundle.BundleFsPersistenceManager
[] - failed to read bundle: 27c8fb7c-b9ef-4b6c-9b59-565d71f51ce5:
java.io.EOFException

The system seems to be scanning the repository forever now and never really gets into a consistent state.