New beginTranscriptFlush step added to turn handoff processing

What

• The main input/query pipeline now checks for a handed-off turn (handedOffTurn) alongside the existing orphaned-permission check when deciding whether to send an initial state message, and it now passes a new beginTranscriptFlush step into the drain logic. The user-input processor also gets a new aheadOfSessionStart flag.
• beginTranscriptFlush itself is a new confirmation wait: it races flushing internal events against an abort signal, and if the flush hasn't been confirmed within 15 seconds, it logs a warning that the session store hasn't confirmed the carried-over lines.

Why This adds a safety check during turn handoff so Claude Code can tell when the session store is slow to confirm it has received carried-over transcript lines, surfacing a warning instead of silently proceeding as if the handoff succeeded.