R1:1da94dcf499e

Correct some issues around IMPORTED_PERMANENT in RefEngine

Summary: Ref T13591. Fixes a few issues with the recent updates here discovered in more thorough testing.

Test Plan:
- Stopped the daemons.
- Created a new copy of Phabricator in Diffusion.
- Pulled it with `bin/repository pull ...`.
- Got 17,278 commits on disk with `git log --all --format=%H`.
- Set permanent refs to "master".
- Discovered it with `bin/repository discover ...`.
- This took 31.5s and inserted 17,278 tasks.
- Verified that…