fix(#690): reconcile watcher startup against the live Explorer

The merged #691 refresh still left files that existed before daemon start
invisible: incrementalLoop seeded its known map from a tree walk, so those
paths looked already-seen and never entered Explorer. Seed from Explorer
instead, reconcile immediately at startup, notify a live daemon after
snapshot, and stop claiming codedb_index is only for never-indexed folders.

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