fix: close three seams the message-machine refactor left open

agent-loop lifecycle: dispose drains machine.done to true quiescence.
cancel()'s own running-to-idle transition can legitimately re-enter
through an automation listener (goal-session's idle drive runs
synchronously to its first await) and replace done with a fresh
admission after the single capture; teardown now re-cancels and
re-awaits until the slot stabilizes, so the scope never unwinds under a
live run.

tools: a nested concludeTurn() stages on its own execution and promotes
to the enclosing composite only on the call's authoritative successful
verdict. A post-execute policy that converts the nested success into an
error no longer lets a recovering composite stop the turn on a failed
terminal operation (the Code Mode structured-output shape).

goal-session: the driver owns its round durability barrier again. The
loop's persistence is eager write-behind with no turn-end flush, so the
old post-turn agent/error signal for flush failures never fires; a
settled round now sets needsCheckpoint and re-enters drive, flushing
before the next reservation and disarming on failure instead of queueing
an autonomous round on state that was never persisted.

packages/core/agent-loop/src/index.ts

@@ -374,7 +374,18 @@ export class AgentLoop extends Service implements AgentFactory {
         if (machine === undefined) await machineReady.promise
         if (machine !== undefined) {
           machine.cancel({ kind: 'disposed' })
-          await Promise.allSettled([machine.done])
+          // Drain to TRUE quiescence: cancel's own synchronous event chain
+          // (running→idle) can legitimately re-enter through an automation
+          // listener (goal-session's idle drive) and replace `done` with a
+          // fresh admission before this await captures it. The replacement
+          // work is cancelled and drained in turn until the slot stabilizes.
+          let done = machine.done
+          while (true) {
+            await Promise.allSettled([done])
+            if (machine.done === done) break
+            done = machine.done
+            machine.cancel({ kind: 'disposed' })
+          }
           await machine.scope.dispose()
         }
       } finally {

packages/core/agent-loop/tests/scope-lifecycle.spec.ts

@@ -1042,4 +1042,43 @@ describe('agent scope lifecycle', () => {
     await ctx.fiber.dispose()
   })
 
+  it('drains a run re-entered by cancel\'s own idle transition before removing the scope', async () => {
+    // Automation shaped like goal-session: the running→idle transition that
+    // disposal's cancel produces immediately queues a follow-up prompt. The
+    // teardown must drain that replacement run to true quiescence instead of
+    // awaiting only the first captured done and unwinding under a live run.
+    const adapter = new MockAdapter([textResponse('one'), textResponse('never awaited')])
+    const ctx = await harness(adapter)
+    const handle = await ctx.agents.create({
+      sessionId: SessionId('drain-reentered-run'),
+      agentOptions: { provider: 'mock', model: 'mock' },
+    })
+    const agent = handle.agent
+    let reentered = false
+    ctx.on('agent/status', (subject, status) => {
+      if (subject !== agent || status !== 'idle' || reentered) return
+      reentered = true
+      agent.followup({ content: [{ type: 'text', text: 'reentrant' }], source: { kind: 'user' } })
+    })
+
+    agent.followup({ content: [{ type: 'text', text: 'go' }], source: { kind: 'user' } })
+    await waitForIdle(ctx, agent)
+    expect(reentered).toBe(true)
+
+    // Idle again: the reentrant admission was already claimed and settled (its
+    // prompt was blocked by nothing, so it ran) — arm a SECOND reentry that
+    // fires from the disposal cancel's idle transition itself.
+    reentered = false
+    await handle.dispose()
+
+    // The reentrant run either never started or was drained: the registries
+    // are empty and nothing still drives the detached session.
+    expect(ctx.agents.get(agent.id)).toBeUndefined()
+    expect(ctx.sessions.get(agent.id)).toBeUndefined()
+    const eventsAfter = agent.session.events.length
+    await new Promise(resolve => setTimeout(resolve, 30))
+    expect(agent.session.events.length).toBe(eventsAfter)
+    await ctx.fiber.dispose()
+  })
+
 })

packages/core/tools/src/index.ts

@@ -657,6 +657,12 @@ export class ToolRegistry extends Service {
   private concludingExecutions = new WeakSet<ToolExecution>()
   /** Enclosing transport tokens marked terminal by a successful nested call. */
   private concludingParents = new Set<ToolExecutionToken>()
+  /**
+   * Nested conclusions staged until their call's final verdict: a post-execute
+   * policy may still convert the nested success into an error, and a failed
+   * terminal operation must not stop the turn through its composite.
+   */
+  private pendingParentConclusions = new WeakMap<ToolRunContext, ToolExecutionToken>()
   /** Original caller cancellation, kept outside the wrapper-mutable execution object. */
   private cancellationStates = new WeakMap<ToolRunContext, ToolCancellationState>()
   /** Definition-owned final content transform snapshotted before policy begins. */
@@ -979,7 +985,7 @@ export class ToolRegistry extends Service {
     const definition = this.get(name, agent)
     const finalizeContent = definition?.finalizeContent?.bind(definition)
     const concludingExecutions = this.concludingExecutions
-    const concludingParents = this.concludingParents
+    const pendingParentConclusions = this.pendingParentConclusions
     const base = {
       token,
       callId,
@@ -992,7 +998,9 @@ export class ToolRegistry extends Service {
       },
       concludeTurn(): void {
         if (parent === undefined) concludingExecutions.add(this as unknown as ToolExecution)
-        else concludingParents.add(parent)
+        // Staged, not propagated: only this nested call's authoritative
+        // successful result promotes the marker onto its parent.
+        else pendingParentConclusions.set(this as unknown as ToolRunContext, parent)
       },
     }
     try {
@@ -1206,6 +1214,14 @@ export class ToolRegistry extends Service {
     } catch (error: unknown) {
       finalResult = this.materializeFinalResult(toolErrorResult(error))
     }
+    // Promote a staged nested conclusion only on the call's authoritative
+    // successful verdict — a policy-converted failure must not let the
+    // composite stop the turn on a failed terminal operation.
+    const stagedParent = this.pendingParentConclusions.get(exec)
+    if (stagedParent !== undefined) {
+      this.pendingParentConclusions.delete(exec)
+      if (!finalResult.isError) this.concludingParents.add(stagedParent)
+    }
     this.notifyResult(exec, finalResult)
     this.concludingParents.delete(exec.token)
     return finalResult

packages/core/tools/tests/tools.spec.ts

@@ -553,6 +553,54 @@ describe('ToolRegistry', () => {
     expect(nested.isError ? undefined : nested.value).toBe('')
   })
 
+  it('propagates a nested concludeTurn only when the nested verdict stays successful', async () => {
+    const ctx = await setup()
+    ctx.tools.register({
+      ...echoTool,
+      name: 'terminal-nested',
+      async execute(_args, exec) {
+        exec.concludeTurn()
+        return 'staged'
+      },
+    })
+    // A composite that swallows its nested failure and returns success — the
+    // Code Mode shape the staged propagation exists for.
+    let call = 0
+    ctx.tools.register({
+      ...echoTool,
+      name: 'composite',
+      async execute(_args, exec) {
+        call += 1
+        const nested = await ctx.tools.execute({
+          signal: exec.signal, callId: CallId(`nested-${call}`), name: 'terminal-nested', arguments: {}, parent: exec.token,
+        })
+        return nested.isError ? 'nested failed, composite recovered' : 'nested succeeded'
+      },
+    })
+
+    // A policy converts the nested success into an error: the staged
+    // conclusion must NOT reach the composite, or the loop would stop the
+    // turn on a failed terminal operation.
+    const veto = ctx.on('tools/post-execute', async (exec, _result, next): Promise<PostToolDecision> => {
+      if (exec.name !== 'terminal-nested') return next()
+      return { kind: 'block', feedback: [{ type: 'text', text: 'nested success rejected' }] }
+    })
+    const recovered = await ctx.tools.execute({
+      signal: testToolSignal, callId: CallId('composite-vetoed'), name: 'composite', arguments: {},
+    })
+    expect(recovered.isError).toBe(false)
+    expect(recovered.concludesTurn).toBeUndefined()
+    veto()
+
+    // The same nested call succeeding promotes the marker: the composite's
+    // own successful result now carries concludesTurn.
+    const concluded = await ctx.tools.execute({
+      signal: testToolSignal, callId: CallId('composite-ok'), name: 'composite', arguments: {},
+    })
+    expect(concluded.isError).toBe(false)
+    expect(concluded.concludesTurn).toBe(true)
+  })
+
   it('returns isError results for unknown tools and throwing tools', async () => {
     const ctx = await setup()
     ctx.tools.register({