fix: warn on config divergence after boot

[brickfrog]

Supersedes PR #580; re-lands the warn-only config divergence check and fixes audit findings F1 empty-project paths, F2 prenotify signature collisions, and F3 full Config coverage.\nVerification: moon test --target native && moon run src/bin/choir_lint --target native passed (2017 tests; lint clean).

Verification

Generated by Choir from commands executed in the leaf workspace.

• moon test --target native
  • exit: 0
  • head: c6dfc6c
  • output tail:

Warning: Main package `choir/src/bin/choir` uses blackbox-only test inputs (`_test.mbt` files) in package directory "/mnt/data/Code/choir/.choir/worktrees/ei4y-audit-fixes-1781376939187-302538-0/src/bin/choir". Main packages will stop generating blackbox tests in a future release. Move public behavior into a non-main package and keep the main package as an entrypoint.
4
Total tests: 2017, passed: 2017, failed: 0.

• moon run src/bin/choir_lint --target native
  • exit: 0
  • head: c6dfc6c

[brickfrog]

Choir: GitHub Actions rollup reports all checks successful on the latest head — re-check review/merge policy on GitHub (not an approval or merge signal by itself).