Gitlab MR stuck on conflicts when there are none

Gitaly log:

Rugged::IndexError: unsupported mandatory extension: 'link'"
***
Rugged::IndexError: invalid data in index - invalid entry"

It looks like libgit2 doesn't support splitindex and that it outputs unsupported mandatory extension: 'link' when it has to read a split index.

The split index just improves performance when rebasing and doing many commits or other operations that result in index writes. So if we can remove it, then it might impact performance a bit for some operations but otherwise things should still work.

A quick patch would be to change true to false on https://gitlab.com/gitlab-org/gitaly/blob/master/ruby/lib/gitlab/git/repository.rb#L865

Related: Zendesk ticket, #1622 (closed), Slack thread.