[codex] fix watcher stale root cleanup

[pcristin]

Summary

• Track consecutive missing project roots in the watcher.
• Preserve projects through transient missing-root checks, then prune after three consecutive misses.
• Delete cached project DB/WAL/SHM files when sustained absence is confirmed.
• Add a regression test covering transient miss preservation and sustained cleanup.

Fixes #286.

Validation

• make -f Makefile.cbm build/c/test-runner passed.
• git diff --check passed.