fix(continuation): auto-continue GPT permission-seeking replies

Resume GPT sessions when the last assistant reply ends in a permission-seeking tail, while honoring stop-continuation and avoiding duplicate continuation across todo and atlas flows.

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

src/hooks/atlas/idle-event.ts

@@ -110,6 +110,7 @@ function scheduleRetry(input: {
     const currentProgress = getPlanProgress(currentBoulder.active_plan)
     if (currentProgress.isComplete) return
     if (options?.isContinuationStopped?.(sessionID)) return
+    if (options?.shouldSkipContinuation?.(sessionID)) return
     if (hasRunningBackgroundTasks(sessionID, options)) return
 
     await injectContinuation({
@@ -192,6 +193,11 @@ export async function handleAtlasSessionIdle(input: {
     return
   }
 
+  if (options?.shouldSkipContinuation?.(sessionID)) {
+    log(`[${HOOK_NAME}] Skipped: another continuation hook already injected`, { sessionID })
+    return
+  }
+
   if (sessionState.lastContinuationInjectedAt && now - sessionState.lastContinuationInjectedAt < CONTINUATION_COOLDOWN_MS) {
     scheduleRetry({ ctx, sessionID, sessionState, options })
     log(`[${HOOK_NAME}] Skipped: continuation cooldown active`, {

src/hooks/atlas/index.test.ts

@@ -1042,6 +1042,37 @@ describe("atlas hook", () => {
        expect(mockInput._promptMock).not.toHaveBeenCalled()
      })
 
+     test("should skip when another continuation hook already injected", async () => {
+       // given - boulder state with incomplete plan
+       const planPath = join(TEST_DIR, "test-plan.md")
+       writeFileSync(planPath, "# Plan\n- [ ] Task 1\n- [ ] Task 2")
+
+       const state: BoulderState = {
+         active_plan: planPath,
+         started_at: "2026-01-02T10:00:00Z",
+         session_ids: [MAIN_SESSION_ID],
+         plan_name: "test-plan",
+       }
+       writeBoulderState(TEST_DIR, state)
+
+       const mockInput = createMockPluginInput()
+       const hook = createAtlasHook(mockInput, {
+         directory: TEST_DIR,
+         shouldSkipContinuation: (sessionID: string) => sessionID === MAIN_SESSION_ID,
+       })
+
+       // when
+       await hook.handler({
+         event: {
+           type: "session.idle",
+           properties: { sessionID: MAIN_SESSION_ID },
+         },
+       })
+
+       // then - should not call prompt because another continuation already handled it
+       expect(mockInput._promptMock).not.toHaveBeenCalled()
+     })
+
     test("should clear abort state on message.updated", async () => {
       // given - boulder with incomplete plan
       const planPath = join(TEST_DIR, "test-plan.md")

src/hooks/atlas/types.ts

@@ -7,6 +7,7 @@ export interface AtlasHookOptions {
   directory: string
   backgroundManager?: BackgroundManager
   isContinuationStopped?: (sessionID: string) => boolean
+  shouldSkipContinuation?: (sessionID: string) => boolean
   agentOverrides?: AgentOverrides
   /** Enable auto-commit after each atomic task completion (default: true) */
   autoCommit?: boolean