Comment 11 for bug 441125

So I've tracked this down to line 1289 in groupcompress_repo.py giving unexpected results:

  file_id_parent_map = source_vf.get_parent_map(self._text_refs)

When run on the stacked branch, self._text_refs has 5024 members in the set, while file_id_parent_map only has 4875 keys. So, lots of them are missing. In comparison, when run on the matching generated branch, self._text_refs has 10372 members and file_id_parent_map has 10372 keys.

At this point, my guess is that this is a bug in reconcile when running on a stacked branch. I'll investigate more next week (unless someone smarter jumps in and solves it).