perf(watcher): skip unchanged dirs and index files on outline miss

The live walker still readdired every directory every 2s, and explicit
refreshIndex re-read every file because seeded mtime was always 0. Cache
directory mtimes so an unchanged listing is not walked, persist file
mtimes on the store so later refreshes skip unread files, and keep
statting known files so in-place edits are still seen.

codedb_outline now indexes a just-added on-disk file on miss instead of
telling the agent to run codedb_index. The leftover not-indexed hint is
only for missing, ignored, or oversized paths.

Co-Authored-By: Codegraff <blackfloofie@codegraff.com>