Enhancement: Make `prune` command resumable

When `prune` was interrupted, it a latter `prune` run previously started repacking
the pack files from the start as `prune` did not update the index while repacking.

The `prune` command now supports resuming interrupted prune runs. The update
of the repository index also has been optimized to use less memory and only
rewrite parts of the index that have changed.

https://github.com/restic/restic/issues/3806
https://github.com/restic/restic/pull/4812