Bugfix: Correctly rebuild index for legacy repositories

After running `rebuild-index` on a legacy repository containing mixed pack
files (that is, pack files which store both metadata and file data), `check`
printed warnings like `pack 12345678 contained in several indexes: ...`.
This warning was not critical, but has now nonetheless been fixed by properly
handling mixed pack files while rebuilding the index.

Running `prune` for such legacy repositories will also fix the warning by
reorganizing the pack files which caused it.

https://github.com/restic/restic/pull/3772
https://github.com/restic/restic/pull/3884
https://forum.restic.net/t/5044/13
