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, "")
 }

src/plugin-handlers/agent-config-handler.ts

@@ -186,6 +186,7 @@ export async function applyAgentConfig(params: {
         pluginPrometheusOverride: prometheusOverride,
         userCategories: params.pluginConfig.categories,
         currentModel,
+        disabledTools: params.pluginConfig.disabled_tools,
       });
     }
 

src/plugin-handlers/prometheus-agent-config-builder.ts

@@ -27,6 +27,7 @@ export async function buildPrometheusAgentConfig(params: {
   pluginPrometheusOverride: PrometheusOverride | undefined;
   userCategories: Record<string, CategoryConfig> | undefined;
   currentModel: string | undefined;
+  disabledTools?: readonly string[];
 }): Promise<Record<string, unknown>> {
   const categoryConfig = params.pluginPrometheusOverride?.category
     ? resolveCategoryConfig(params.pluginPrometheusOverride.category, params.userCategories)
@@ -69,7 +70,7 @@ export async function buildPrometheusAgentConfig(params: {
     ...(resolvedModel ? { model: resolvedModel } : {}),
     ...(variantToUse ? { variant: variantToUse } : {}),
     mode: "all",
-    prompt: getPrometheusPrompt(resolvedModel),
+    prompt: getPrometheusPrompt(resolvedModel, params.disabledTools),
     permission: PROMETHEUS_PERMISSION,
     description: `${(params.configAgentPlan?.description as string) ?? "Plan agent"} (Prometheus - OhMyOpenCode)`,
     color: (params.configAgentPlan?.color as string) ?? "#FF5722",

src/plugin-handlers/tool-config-handler.test.ts

@@ -5,6 +5,7 @@ import type { OhMyOpenCodeConfig } from "../config"
 function createParams(overrides: {
   taskSystem?: boolean
   agents?: string[]
+  disabledTools?: string[]
 }) {
   const agentResult: Record<string, { permission?: Record<string, unknown> }> = {}
   for (const agent of overrides.agents ?? []) {
@@ -15,6 +16,7 @@ function createParams(overrides: {
     config: { tools: {}, permission: {} } as Record<string, unknown>,
     pluginConfig: {
       experimental: { task_system: overrides.taskSystem ?? false },
+      disabled_tools: overrides.disabledTools,
     } as OhMyOpenCodeConfig,
     agentResult: agentResult as Record<string, unknown>,
   }
@@ -183,4 +185,86 @@ describe("applyToolConfig", () => {
       })
     })
   })
+
+  describe("#given disabled_tools includes 'question'", () => {
+    let originalConfigContent: string | undefined
+    let originalCliRunMode: string | undefined
+
+    beforeEach(() => {
+      originalConfigContent = process.env.OPENCODE_CONFIG_CONTENT
+      originalCliRunMode = process.env.OPENCODE_CLI_RUN_MODE
+      delete process.env.OPENCODE_CONFIG_CONTENT
+      delete process.env.OPENCODE_CLI_RUN_MODE
+    })
+
+    afterEach(() => {
+      if (originalConfigContent === undefined) {
+        delete process.env.OPENCODE_CONFIG_CONTENT
+      } else {
+        process.env.OPENCODE_CONFIG_CONTENT = originalConfigContent
+      }
+      if (originalCliRunMode === undefined) {
+        delete process.env.OPENCODE_CLI_RUN_MODE
+      } else {
+        process.env.OPENCODE_CLI_RUN_MODE = originalCliRunMode
+      }
+    })
+
+    describe("#when question is in disabled_tools", () => {
+      it.each(["sisyphus", "hephaestus", "prometheus"])(
+        "#then should deny question for %s agent",
+        (agentName) => {
+          const params = createParams({
+            agents: [agentName],
+            disabledTools: ["question"],
+          })
+
+          applyToolConfig(params)
+
+          const agent = params.agentResult[agentName] as {
+            permission: Record<string, unknown>
+          }
+          expect(agent.permission.question).toBe("deny")
+        },
+      )
+    })
+
+    describe("#when question is in disabled_tools alongside other tools", () => {
+      it.each(["sisyphus", "hephaestus", "prometheus"])(
+        "#then should deny question for %s agent",
+        (agentName) => {
+          const params = createParams({
+            agents: [agentName],
+            disabledTools: ["todowrite", "question", "interactive_bash"],
+          })
+
+          applyToolConfig(params)
+
+          const agent = params.agentResult[agentName] as {
+            permission: Record<string, unknown>
+          }
+          expect(agent.permission.question).toBe("deny")
+        },
+      )
+    })
+
+    describe("#when disabled_tools does not include question", () => {
+      it.each(["sisyphus", "hephaestus", "prometheus"])(
+        "#then should allow question for %s agent",
+        (agentName) => {
+          const params = createParams({
+            agents: [agentName],
+            disabledTools: ["todowrite", "interactive_bash"],
+          })
+
+          applyToolConfig(params)
+
+          const agent = params.agentResult[agentName] as {
+            permission: Record<string, unknown>
+          }
+          expect(agent.permission.question).toBe("allow")
+        },
+      )
+    })
+  })
 })

src/plugin-handlers/tool-config-handler.ts

@@ -44,7 +44,9 @@ export function applyToolConfig(params: {
 
   const isCliRunMode = process.env.OPENCODE_CLI_RUN_MODE === "true";
   const configQuestionPermission = getConfigQuestionPermission();
+  const isQuestionDisabledByPlugin = params.pluginConfig.disabled_tools?.includes("question") ?? false;
   const questionPermission =
+    isQuestionDisabledByPlugin ? "deny" :
     configQuestionPermission === "deny" ? "deny" :
     isCliRunMode ? "deny" :
     "allow";