Closes (partially) #70319.

Summary

Introduces a per-session run-generation counter that layers on top of the existing abort primitives (replyRunRegistry, abortEmbeddedPiRun, chat.abort, cancelScope) to provide a unified invalidation signal downstream code can consult before producing side effects.

Goal from the issue: after /stop or a new user message, the superseded run must not produce more output — tool calls, deltas, typing, final replies.

This PR ships the foundation (Pieces A + partial C from the issue's implementation sketch) and wires one real emission site so the fence is live.

What's in this PR

Piece A — Run generation registry (new)

src/auto-reply/reply/run-generation.ts: getCurrentGeneration, incrementGeneration, isCurrentGeneration, forgetGeneration. Global-singleton backed.

Piece A wiring — ReplyOperation carries the generation

• ReplyOperation.runGeneration captured at createReplyOperation.
• ReplyOperation.isCurrent() convenience wrapper over isCurrentGeneration(key, runGeneration).
• abortWithReason in the registry bumps the generation, so any abortByUser / abortForRestart path invalidates the captured value.

Fast-abort integration

tryFastAbortFromMessage in abort.ts also bumps generation up-front so /stop fences late output even when the registry lookup misses (race between end-of-run and the stop message).

Piece C — Stale-output fence (partial, opt-in)

createBlockReplyDeliveryHandler accepts an optional isRunCurrent?: () => boolean parameter. When provided and returns false, the block reply is silently dropped before hitting the channel. Callers pass () => replyOperation.isCurrent().

Live wiring

agent-runner-execution.ts passes the fence callback so post-abort block replies are actually dropped in the real runtime.

Piece D — SIGTERM→SIGKILL escalation

Already covered by src/process/kill-tree.test.ts. No change needed.

What's explicitly deferred

• Piece B (pre-tool gate): wiring into pi-embedded-runner's tool dispatch. Pattern demonstrated in tests; wiring-only follow-up.
• Piece E (new-message takeover): dispatch.ts / queue.ts integration. The primitive (incrementGeneration) is in place.
• More emission sites: typing.ts, reply-delivery for non-block path, followup-delivery.ts. Same opt-in shape.

Tests

src/auto-reply/reply/run-generation.test.ts — 17 tests covering:

• Registry primitives.
• ReplyOperation generation wiring (capture at begin, flip on abort, next run captures new gen).
• Stale-output fence pattern (Tests 2, 3, 5 from the issue).
• Integration with createBlockReplyDeliveryHandler.

pnpm check:changed  → exit 0
  typecheck core    → ok
  typecheck tests   → ok
  lint core         → ok
  import cycles     → ok
  guards            → ok
  auto-reply suite  → 102 files / 1174 tests passed

pnpm build also passes clean.

Constraints honored

• No change to gateway protocol.
• No modification to AGENTS.md / CONTRIBUTING.md / CLAUDE.md.
• Existing abort behavior unchanged — the new system layers on top.
• TypeScript ESM, strict types, no any.
• American English in code/comments.

Happy to break into smaller commits or reshape if the approach lands differently than maintainers prefer.