Correct some issues around IMPORTED_PERMANENT in RefEngine
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Description

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 all tasks have priority 4,000 (PRIORITY_IMPORT).
- Observed that 16,799 commits have IMPORTED_PERMANENT and 479 commits do not.
  - This matches git log master --format=%H exactly.
Ran bin/repository refs .... Expected no changes and saw no changes.
Ran bin/worker execute --active for a minute or two. It processed all the impermanent changes first (since bin/worker is LIFO and these are supposed to process last).
- Ran bin/repository refs. Expected no changes and saw no changes.
- Marked all refs as permanent.
- Starting state: 16,009 message tasks, all at priority 4000.
- Ran bin/repository refs, expecting 479 new tasks at priority 4000.
- Saw count rise to 16,488 as expected.
- Saw all the new tasks have priority 4000 and all commits now have the IMPORTED_PERMANENT flag.