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) })
   }

src/hooks/todo-continuation-enforcer/pending-question-detection.test.ts

@@ -0,0 +1,100 @@
+/// <reference types="bun-types" />
+import { describe, expect, test } from "bun:test"
+
+import { hasUnansweredQuestion } from "./pending-question-detection"
+
+describe("hasUnansweredQuestion", () => {
+  test("given empty messages, returns false", () => {
+    expect(hasUnansweredQuestion([])).toBe(false)
+  })
+
+  test("given null-ish input, returns false", () => {
+    expect(hasUnansweredQuestion(undefined as never)).toBe(false)
+  })
+
+  test("given last assistant message with question tool_use, returns true", () => {
+    const messages = [
+      { info: { role: "user" } },
+      {
+        info: { role: "assistant" },
+        parts: [
+          { type: "tool_use", name: "question" },
+        ],
+      },
+    ]
+    expect(hasUnansweredQuestion(messages)).toBe(true)
+  })
+
+  test("given last assistant message with question tool-invocation, returns true", () => {
+    const messages = [
+      { info: { role: "user" } },
+      {
+        info: { role: "assistant" },
+        parts: [
+          { type: "tool-invocation", toolName: "question" },
+        ],
+      },
+    ]
+    expect(hasUnansweredQuestion(messages)).toBe(true)
+  })
+
+  test("given user message after question (answered), returns false", () => {
+    const messages = [
+      {
+        info: { role: "assistant" },
+        parts: [
+          { type: "tool_use", name: "question" },
+        ],
+      },
+      { info: { role: "user" } },
+    ]
+    expect(hasUnansweredQuestion(messages)).toBe(false)
+  })
+
+  test("given assistant message with non-question tool, returns false", () => {
+    const messages = [
+      { info: { role: "user" } },
+      {
+        info: { role: "assistant" },
+        parts: [
+          { type: "tool_use", name: "bash" },
+        ],
+      },
+    ]
+    expect(hasUnansweredQuestion(messages)).toBe(false)
+  })
+
+  test("given assistant message with no parts, returns false", () => {
+    const messages = [
+      { info: { role: "user" } },
+      { info: { role: "assistant" } },
+    ]
+    expect(hasUnansweredQuestion(messages)).toBe(false)
+  })
+
+  test("given role on message directly (not in info), returns true for question", () => {
+    const messages = [
+      { role: "user" },
+      {
+        role: "assistant",
+        parts: [
+          { type: "tool_use", name: "question" },
+        ],
+      },
+    ]
+    expect(hasUnansweredQuestion(messages)).toBe(true)
+  })
+
+  test("given mixed tools including question, returns true", () => {
+    const messages = [
+      {
+        info: { role: "assistant" },
+        parts: [
+          { type: "tool_use", name: "bash" },
+          { type: "tool_use", name: "question" },
+        ],
+      },
+    ]
+    expect(hasUnansweredQuestion(messages)).toBe(true)
+  })
+})

src/hooks/todo-continuation-enforcer/pending-question-detection.ts

@@ -0,0 +1,40 @@
+import { log } from "../../shared/logger"
+import { HOOK_NAME } from "./constants"
+
+interface MessagePart {
+  type: string
+  name?: string
+  toolName?: string
+}
+
+interface Message {
+  info?: { role?: string }
+  role?: string
+  parts?: MessagePart[]
+}
+
+export function hasUnansweredQuestion(messages: Message[]): boolean {
+  if (!messages || messages.length === 0) return false
+
+  for (let i = messages.length - 1; i >= 0; i--) {
+    const msg = messages[i]
+    const role = msg.info?.role ?? msg.role
+
+    if (role === "user") return false
+
+    if (role === "assistant" && msg.parts) {
+      const hasQuestion = msg.parts.some(
+        (part) =>
+          (part.type === "tool_use" || part.type === "tool-invocation") &&
+          (part.name === "question" || part.toolName === "question"),
+      )
+      if (hasQuestion) {
+        log(`[${HOOK_NAME}] Detected pending question tool in last assistant message`)
+        return true
+      }
+      return false
+    }
+  }
+
+  return false
+}