Publish and Initialize now re-emit the project shell after refreshing its
identity, as clone completion does, so connected clients see the new
repository without a reload. Turn-end PR discovery keeps the snapshot's
identity when the refresh fails, so a transient git error cannot drop a
thread from backfill.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WvDgDwRRG8xvtoABQ8KwtC