put ent issue database in a dir in the main branches?

Currently entomologist can access an issue database in a branch (via
temporary worktrees), or in a directory (via direct access).

The directory-based issue database mode is kind of broken, because
entomologist blindly runs `git commit` after modifying the database
(and isn't careful about managing the git index when doing so).

(Tangent: The IssueDatabase and IssueDatabaseSource structs of the `ent`
binary should maybe move into the lib Issues struct, and the code could
make smarter choices about how to access the database.)

Putting the entomologist issue database in the main branch(es) of the
repo has some appealing qualities.  For example, a bug-fix branch could
both fix the bug in the code, and change the bug's issue status from
"InProgress" to "Done", so that when the branch is merged to main,
the bug gets fixed there.

The branch can be rebased on top of main to pick up changes to the bug.