Ephemeral empty-response/prefill recovery scaffolding (the synthetic
assistant "(empty)" turn, the user nudge, the terminal "(empty)"
sentinel, and the thinking-only prefill placeholder) exists only to
drive the next API retry; the in-memory loop pops it before appending
the real response. The append-only flush did not mirror that, so a
mid-turn persist could commit scaffolding to the SQLite session store
(and JSON log), and a resumed session would replay synthetic
"(empty)"/nudge turns as genuine context — re-poisoning the empty-retry
boundary forever.
Filter ephemeral scaffolding at both durable-write sites
(_flush_messages_to_session_db + _save_session_log), by flag not
position, so buried scaffolding (an answered nudge leaves the synthetic
pair mid-list) is skipped too. Covers all three flags including
_thinking_prefill.
Adapted onto current main's identity-tracking flush.
Cherry-picked from #41281 by petrichor-op.
f2a528fb59