Bugfix: Correctly rebuild index for legacy repositories

After running `rebuild-index` on a legacy repository containing mixed pack
files, that is pack files with store both metadata and file data, `check`
printed warnings like `pack 12345678 contained in several indexes: ...`.  The
warning is not critical. It has 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 cause the warning.

https://github.com/restic/restic/pull/3772
https://forum.restic.net/t/help-in-recovery-a-corrupted-repository/5044/13