fix: respect disabled_tools config in agent prompts (fixes #2742)

- Check disabled_tools for 'question' in tool-config-handler permission logic
- Strip Question tool code examples from Prometheus prompts when disabled
- Pass disabled_tools through prometheus agent config builder pipeline
- Add tests for disabled_tools question permission handling

src/agents/prometheus/system-prompt.test.ts

@@ -0,0 +1,42 @@
+import { describe, it, expect } from "bun:test"
+import { getPrometheusPrompt } from "./system-prompt"
+
+describe("getPrometheusPrompt", () => {
+  describe("#given question tool is not disabled", () => {
+    describe("#when generating prompt", () => {
+      it("#then should include Question tool references", () => {
+        const prompt = getPrometheusPrompt(undefined, [])
+
+        expect(prompt).toContain("Question({")
+      })
+    })
+  })
+
+  describe("#given question tool is disabled via disabled_tools", () => {
+    describe("#when generating prompt", () => {
+      it("#then should strip Question tool code examples", () => {
+        const prompt = getPrometheusPrompt(undefined, ["question"])
+
+        expect(prompt).not.toContain("Question({")
+      })
+    })
+
+    describe("#when disabled_tools includes question among other tools", () => {
+      it("#then should strip Question tool code examples", () => {
+        const prompt = getPrometheusPrompt(undefined, ["todowrite", "question", "interactive_bash"])
+
+        expect(prompt).not.toContain("Question({")
+      })
+    })
+  })
+
+  describe("#given no disabled_tools provided", () => {
+    describe("#when generating prompt with undefined", () => {
+      it("#then should include Question tool references", () => {
+        const prompt = getPrometheusPrompt(undefined, undefined)
+
+        expect(prompt).toContain("Question({")
+      })
+    })
+  })
+})

src/agents/prometheus/system-prompt.ts

@@ -52,16 +52,34 @@ export function getPrometheusPromptSource(model?: string): PrometheusPromptSourc
  * Gemini models → Gemini-optimized prompt (aggressive tool-call enforcement, thinking checkpoints)
  * Default (Claude, etc.) → Claude-optimized prompt (modular sections)
  */
-export function getPrometheusPrompt(model?: string): string {
+export function getPrometheusPrompt(model?: string, disabledTools?: readonly string[]): string {
   const source = getPrometheusPromptSource(model)
+  const isQuestionDisabled = disabledTools?.includes("question") ?? false
 
+  let prompt: string
   switch (source) {
     case "gpt":
-      return getGptPrometheusPrompt()
+      prompt = getGptPrometheusPrompt()
+      break
     case "gemini":
-      return getGeminiPrometheusPrompt()
+      prompt = getGeminiPrometheusPrompt()
+      break
     case "default":
     default:
-      return PROMETHEUS_SYSTEM_PROMPT
+      prompt = PROMETHEUS_SYSTEM_PROMPT
   }
+
+  if (isQuestionDisabled) {
+    prompt = stripQuestionToolReferences(prompt)
+  }
+
+  return prompt
+}
+
+/**
+ * Removes Question tool usage examples from prompt text when question tool is disabled.
+ */
+function stripQuestionToolReferences(prompt: string): string {
+  // Remove Question({...}) code blocks (multi-line)
+  return prompt.replace(/```typescript\n\s*Question\(\{[\s\S]*?\}\)\s*\n```/g, "")
 }