Merge branch 'js/shallow-and-fetch-prune' into maint

Merge branch 'js/shallow-and-fetch-prune' into maint

"git repack" in a shallow clone did not correctly update the
shallow points in the repository, leading to a repository that
does not pass fsck.

* js/shallow-and-fetch-prune:
  repack -ad: prune the list of shallow commits
  shallow: offer to prune only non-existing entries
  repack: point out a bug handling stale shallow info