bugfix: reindexing is not necessary for DB v0.9.3 to v5 upgrade (#13434)

reindexing takes a significant amount of time, and there's no reason to
do it from DB version 0.9.3 to version 5. The only difference is that v5
can contain "deprecated_for" fields.

- [x] Add a `_skip_reindex` list at the start of `database.py`

- [x] Skip the reindex for upgrades in this list. The new version will
  just be written to the file the first time we actually have to write
  the DB out (e.g., after an install), and reads will still work fine.