Fix compactInFlight session leak, cache branch entry index, back off zero-chunk observer re-fires

[kaushikvira]

Fixes

1. compactInFlight flag leak (real bug) — in the compaction trigger, the in-flight flag is reset only via ctx.compact()'s onComplete/onError callbacks and a catch. If the captured ctx goes stale (session replacement) and compaction neither completes nor throws, the flag leaks true for the process lifetime and proactive compaction is permanently disabled. The flag is now keyed to a session generation token (session id, falling back to session file); a stale flag whose generation no longer matches is discarded (with a UI note) instead of silently blocking.

2. Per-turn O(n) entry-index rebuilds (perf) — entryIndexById rebuilt a full-branch id→index Map on every call; the per-turn consolidation trigger (agent_start/turn_end) and the agent_settled compaction trigger hit it 3-4 times per event. The Map is now cached keyed by branch tip + length (the branch only grows by appends, so tip/length change is the invalidation signal). Callers are read-only, behavior is identical. (The [...messages].reverse() copy called out in the audit no longer exists on master — the retry-detection block was removed when the trigger moved to agent_settled.)

3. Observer zero-chunk re-fire (nit) — in the consolidation trigger, the empty-chunk path (!chunk.trim()) returned "continue" without arming the deliberate-empty backoff, so a zero-chunk backlog re-fired the observer pipeline every turn. It now arms the same observerEmptyBackoff as the deliberate-empty verdict (Observer re-fires every turn (warning spam) when it returns no observations #23).

Verification

• npm run typecheck — exit 0
• npm test — 261/261 passing, including new regression tests for all three fixes
• No changes to LLM stage thresholds/config defaults; no dependency changes

Addresses audit findings for the installed 3.0.4 package.