fix: resolve issues #1888, #1693, #1891

- fix(hooks): skip todo continuation when agent has pending question (#1888)
  Add pending-question-detection module that walks messages backwards
  to detect unanswered question tool_use, preventing CONTINUATION_PROMPT
  injection while awaiting user response.

- fix(config): allow custom agent names in disabled_agents (#1693)
  Change disabled_agents schema from BuiltinAgentNameSchema to z.string()
  and add filterDisabledAgents helper in agent-config-handler to filter
  user, project, and plugin agents with case-insensitive matching.

- fix(agents): change primary agents mode to 'all' (#1891)
  Update Sisyphus, Hephaestus, and Atlas agent modes from 'primary'
  to 'all' so they are available for @mention routing and task()
  delegation in addition to direct chat.

src/hooks/todo-continuation-enforcer/idle-event.ts

@@ -15,6 +15,7 @@ import {
   MAX_CONSECUTIVE_FAILURES,
 } from "./constants"
 import { isLastAssistantMessageAborted } from "./abort-detection"
+import { hasUnansweredQuestion } from "./pending-question-detection"
 import { getIncompleteCount } from "./todo"
 import type { MessageInfo, ResolvedMessageInfo, Todo } from "./types"
 import type { SessionStateStore } from "./session-state"
@@ -74,6 +75,10 @@ export async function handleSessionIdle(args: {
       log(`[${HOOK_NAME}] Skipped: last assistant message was aborted (API fallback)`, { sessionID })
       return
     }
+    if (hasUnansweredQuestion(messages)) {
+      log(`[${HOOK_NAME}] Skipped: pending question awaiting user response`, { sessionID })
+      return
+    }
   } catch (error) {
     log(`[${HOOK_NAME}] Messages fetch failed, continuing`, { sessionID, error: String(error) })
   }