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/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
+}