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/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")