Cannot Repo Sync Against 9.0 R2

[BrokenE39]

I'm trying to rebuild my VM build machine after it got corrupted and died. When I try to run repo sync, I'm getting these error message:

Checking out projects:  94% (524/557) platform/system/chreerror: Cannot checkout platform/system/gatekeeper: GitError: platform/system/gatekeeper rev-list (u'^0d9bdfd2cbfb2ce13f16c49edb9169e4866d1d57', 'HEAD', '--'): fatal: not a git repository (or any of the parent directories): .git

Traceback (most recent call last):
  File "/home/daniel/android9/.repo/repo/main.py", line 628, in <module>
    _Main(sys.argv[1:])
  File "/home/daniel/android9/.repo/repo/main.py", line 602, in _Main
    result = run()
  File "/home/daniel/android9/.repo/repo/main.py", line 595, in <lambda>
    run = lambda: repo._Run(name, gopts, argv) or 0
  File "/home/daniel/android9/.repo/repo/main.py", line 264, in _Run
    result = cmd.Execute(copts, cargs)
  File "/home/daniel/android9/.repo/repo/subcmds/sync.py", line 982, in Execute
    self._Checkout(all_projects, opt, err_event, err_results)
  File "/home/daniel/android9/.repo/repo/subcmds/sync.py", line 567, in _Checkout
    self._CheckoutWorker(**kwargs)
  File "/home/daniel/android9/.repo/repo/subcmds/sync.py", line 447, in _CheckoutWorker
    return self._CheckoutOne(opt, project, *args, **kwargs)
  File "/home/daniel/android9/.repo/repo/subcmds/sync.py", line 481, in _CheckoutOne
    project.Sync_LocalHalf(syncbuf, force_sync=opt.force_sync)
  File "/home/daniel/android9/.repo/repo/project.py", line 1662, in Sync_LocalHalf
    lost = self._revlist(not_rev(revid), HEAD)
  File "/home/daniel/android9/.repo/repo/project.py", line 3156, in _revlist
    return self.work_git.rev_list(*a, **kw)
  File "/home/daniel/android9/.repo/repo/project.py", line 3367, in rev_list
    (self._project.name, str(args), p.stderr))
error.GitError: platform/system/gatekeeper rev-list (u'^0d9bdfd2cbfb2ce13f16c49edb9169e4866d1d57', 'HEAD', '--'): fatal: not a git repository (or any of the parent directories): .git

This was working a few days ago so I'm not sure if something went wrong with the repo in github.