Bugfix: Fix `prune`, only include existing files in indexes

A bug was found (and corrected) in the index rebuilding after prune, which led
to indexes which include blobs that were not present in the repo any more.
There were already checks in place which detected this situation and aborted
with an error message. A new run of either `prune` or `rebuild-index` corrected
the index files. This is now fixed and a test has been added to detect this.

https://github.com/restic/restic/pull/1115