feat(core): Remove legacy settings. (#17244)

docs/cli/settings.md

@@ -113,14 +113,11 @@ they appear in the UI.
 
 ### Experimental
 
-| UI Label                            | Setting                                                 | Description                                                                         | Default |
+| UI Label         | Setting                      | Description                                                                         | Default |
-| ----------------------------------- | ------------------------------------------------------- | ----------------------------------------------------------------------------------- | ------- |
+| ---------------- | ---------------------------- | ----------------------------------------------------------------------------------- | ------- |
-| Agent Skills                        | `experimental.skills`                                   | Enable Agent Skills (experimental).                                                 | `false` |
+| Agent Skills     | `experimental.skills`        | Enable Agent Skills (experimental).                                                 | `false` |
-| Enable Codebase Investigator        | `experimental.codebaseInvestigatorSettings.enabled`     | Enable the Codebase Investigator agent.                                             | `true`  |
+| Use OSC 52 Paste | `experimental.useOSC52Paste` | Use OSC 52 sequence for pasting instead of clipboardy (useful for remote sessions). | `false` |
-| Codebase Investigator Max Num Turns | `experimental.codebaseInvestigatorSettings.maxNumTurns` | Maximum number of turns for the Codebase Investigator agent.                        | `10`    |
+| Plan             | `experimental.plan`          | Enable planning features (Plan Mode and tools).                                     | `false` |
-| Use OSC 52 Paste                    | `experimental.useOSC52Paste`                            | Use OSC 52 sequence for pasting instead of clipboardy (useful for remote sessions). | `false` |
-| Enable CLI Help Agent               | `experimental.cliHelpAgentSettings.enabled`             | Enable the CLI Help Agent.                                                          | `true`  |
-| Plan                                | `experimental.plan`                                     | Enable planning features (Plan Mode and tools).                                     | `false` |
 
 ### HooksConfig
 

docs/get-started/configuration.md

@@ -855,43 +855,11 @@ their corresponding top-level category object in your `settings.json` file.
   - **Default:** `false`
   - **Requires restart:** Yes
 
-- **`experimental.codebaseInvestigatorSettings.enabled`** (boolean):
-  - **Description:** Enable the Codebase Investigator agent.
-  - **Default:** `true`
-  - **Requires restart:** Yes
-
-- **`experimental.codebaseInvestigatorSettings.maxNumTurns`** (number):
-  - **Description:** Maximum number of turns for the Codebase Investigator
-    agent.
-  - **Default:** `10`
-  - **Requires restart:** Yes
-
-- **`experimental.codebaseInvestigatorSettings.maxTimeMinutes`** (number):
-  - **Description:** Maximum time for the Codebase Investigator agent (in
-    minutes).
-  - **Default:** `3`
-  - **Requires restart:** Yes
-
-- **`experimental.codebaseInvestigatorSettings.thinkingBudget`** (number):
-  - **Description:** The thinking budget for the Codebase Investigator agent.
-  - **Default:** `8192`
-  - **Requires restart:** Yes
-
-- **`experimental.codebaseInvestigatorSettings.model`** (string):
-  - **Description:** The model to use for the Codebase Investigator agent.
-  - **Default:** `"auto"`
-  - **Requires restart:** Yes
-
 - **`experimental.useOSC52Paste`** (boolean):
   - **Description:** Use OSC 52 sequence for pasting instead of clipboardy
     (useful for remote sessions).
   - **Default:** `false`
 
-- **`experimental.cliHelpAgentSettings.enabled`** (boolean):
-  - **Description:** Enable the CLI Help Agent.
-  - **Default:** `true`
-  - **Requires restart:** Yes
-
 - **`experimental.plan`** (boolean):
   - **Description:** Enable planning features (Plan Mode and tools).
   - **Default:** `false`

packages/cli/src/config/config.ts

@@ -764,9 +764,6 @@ export async function loadCliConfig(
     output: {
       format: (argv.outputFormat ?? settings.output?.format) as OutputFormat,
     },
-    codebaseInvestigatorSettings:
-      settings.experimental?.codebaseInvestigatorSettings,
-    cliHelpAgentSettings: settings.experimental?.cliHelpAgentSettings,
     fakeResponses: argv.fakeResponses,
     recordResponses: argv.recordResponses,
     retryFetchErrors: settings.general?.retryFetchErrors,

packages/cli/src/config/settings.test.ts

@@ -2012,6 +2012,56 @@ describe('Settings Loading and Merging', () => {
       // Merged should also reflect it (system overrides defaults, but both are migrated)
       expect(settings.merged.general?.enableAutoUpdateNotification).toBe(false);
     });
+
+    it('should migrate experimental agent settings to agents overrides', () => {
+      const userSettingsContent = {
+        experimental: {
+          codebaseInvestigatorSettings: {
+            enabled: true,
+            maxNumTurns: 15,
+            maxTimeMinutes: 5,
+            thinkingBudget: 16384,
+            model: 'gemini-1.5-pro',
+          },
+          cliHelpAgentSettings: {
+            enabled: false,
+          },
+        },
+      };
+
+      vi.mocked(fs.existsSync).mockReturnValue(true);
+      (fs.readFileSync as Mock).mockImplementation(
+        (p: fs.PathOrFileDescriptor) => {
+          if (p === USER_SETTINGS_PATH)
+            return JSON.stringify(userSettingsContent);
+          return '{}';
+        },
+      );
+
+      const settings = loadSettings(MOCK_WORKSPACE_DIR);
+
+      // Verify migration to agents.overrides
+      expect(settings.user.settings.agents?.overrides).toMatchObject({
+        codebase_investigator: {
+          enabled: true,
+          runConfig: {
+            maxTurns: 15,
+            maxTimeMinutes: 5,
+          },
+          modelConfig: {
+            model: 'gemini-1.5-pro',
+            generateContentConfig: {
+              thinkingConfig: {
+                thinkingBudget: 16384,
+              },
+            },
+          },
+        },
+        cli_help: {
+          enabled: false,
+        },
+      });
+    });
   });
 
   describe('saveSettings', () => {

packages/cli/src/config/settings.ts

@@ -804,6 +804,14 @@ export function migrateDeprecatedSettings(
         anyModified = true;
       }
     }
+
+    // Migrate experimental agent settings
+    anyModified ||= migrateExperimentalSettings(
+      settings,
+      loadedSettings,
+      scope,
+      removeDeprecated,
+    );
   };
 
   processScope(SettingScope.User);
@@ -852,3 +860,100 @@ export function saveModelChange(
     );
   }
 }
+
+function migrateExperimentalSettings(
+  settings: Settings,
+  loadedSettings: LoadedSettings,
+  scope: LoadableSettingScope,
+  removeDeprecated: boolean,
+): boolean {
+  const experimentalSettings = settings.experimental as
+    | Record<string, unknown>
+    | undefined;
+  if (experimentalSettings) {
+    const agentsSettings = {
+      ...(settings.agents as Record<string, unknown> | undefined),
+    };
+    const agentsOverrides = {
+      ...((agentsSettings['overrides'] as Record<string, unknown>) || {}),
+    };
+    let modified = false;
+
+    // Migrate codebaseInvestigatorSettings -> agents.overrides.codebase_investigator
+    if (experimentalSettings['codebaseInvestigatorSettings']) {
+      const old = experimentalSettings[
+        'codebaseInvestigatorSettings'
+      ] as Record<string, unknown>;
+      const override = {
+        ...(agentsOverrides['codebase_investigator'] as
+          | Record<string, unknown>
+          | undefined),
+      };
+
+      if (old['enabled'] !== undefined) override['enabled'] = old['enabled'];
+
+      const runConfig = {
+        ...(override['runConfig'] as Record<string, unknown> | undefined),
+      };
+      if (old['maxNumTurns'] !== undefined)
+        runConfig['maxTurns'] = old['maxNumTurns'];
+      if (old['maxTimeMinutes'] !== undefined)
+        runConfig['maxTimeMinutes'] = old['maxTimeMinutes'];
+      if (Object.keys(runConfig).length > 0) override['runConfig'] = runConfig;
+
+      if (old['model'] !== undefined || old['thinkingBudget'] !== undefined) {
+        const modelConfig = {
+          ...(override['modelConfig'] as Record<string, unknown> | undefined),
+        };
+        if (old['model'] !== undefined) modelConfig['model'] = old['model'];
+        if (old['thinkingBudget'] !== undefined) {
+          const generateContentConfig = {
+            ...(modelConfig['generateContentConfig'] as
+              | Record<string, unknown>
+              | undefined),
+          };
+          const thinkingConfig = {
+            ...(generateContentConfig['thinkingConfig'] as
+              | Record<string, unknown>
+              | undefined),
+          };
+          thinkingConfig['thinkingBudget'] = old['thinkingBudget'];
+          generateContentConfig['thinkingConfig'] = thinkingConfig;
+          modelConfig['generateContentConfig'] = generateContentConfig;
+        }
+        override['modelConfig'] = modelConfig;
+      }
+
+      agentsOverrides['codebase_investigator'] = override;
+      modified = true;
+    }
+
+    // Migrate cliHelpAgentSettings -> agents.overrides.cli_help
+    if (experimentalSettings['cliHelpAgentSettings']) {
+      const old = experimentalSettings['cliHelpAgentSettings'] as Record<
+        string,
+        unknown
+      >;
+      const override = {
+        ...(agentsOverrides['cli_help'] as Record<string, unknown> | undefined),
+      };
+      if (old['enabled'] !== undefined) override['enabled'] = old['enabled'];
+      agentsOverrides['cli_help'] = override;
+      modified = true;
+    }
+
+    if (modified) {
+      agentsSettings['overrides'] = agentsOverrides;
+      loadedSettings.setValue(scope, 'agents', agentsSettings);
+
+      if (removeDeprecated) {
+        const newExperimental = { ...experimentalSettings };
+        delete newExperimental['codebaseInvestigatorSettings'];
+        delete newExperimental['cliHelpAgentSettings'];
+        loadedSettings.setValue(scope, 'experimental', newExperimental);
+      }
+      return true;
+    }
+  }
+  return false;
+}

packages/cli/src/config/settingsSchema.ts

@@ -20,7 +20,6 @@ import {
   DEFAULT_TRUNCATE_TOOL_OUTPUT_LINES,
   DEFAULT_TRUNCATE_TOOL_OUTPUT_THRESHOLD,
   DEFAULT_MODEL_CONFIGS,
-  GEMINI_MODEL_ALIAS_AUTO,
 } from '@google/gemini-cli-core';
 import type { CustomTheme } from '../ui/themes/theme.js';
 import type { SessionRetentionSettings } from './settings.js';
@@ -1461,66 +1460,6 @@ const SETTINGS_SCHEMA = {
         description: 'Enable Agent Skills (experimental).',
         showInDialog: true,
       },
-      codebaseInvestigatorSettings: {
-        type: 'object',
-        label: 'Codebase Investigator Settings',
-        category: 'Experimental',
-        requiresRestart: true,
-        default: {},
-        description: 'Configuration for Codebase Investigator.',
-        showInDialog: false,
-        properties: {
-          enabled: {
-            type: 'boolean',
-            label: 'Enable Codebase Investigator',
-            category: 'Experimental',
-            requiresRestart: true,
-            default: true,
-            description: 'Enable the Codebase Investigator agent.',
-            showInDialog: true,
-          },
-          maxNumTurns: {
-            type: 'number',
-            label: 'Codebase Investigator Max Num Turns',
-            category: 'Experimental',
-            requiresRestart: true,
-            default: 10,
-            description:
-              'Maximum number of turns for the Codebase Investigator agent.',
-            showInDialog: true,
-          },
-          maxTimeMinutes: {
-            type: 'number',
-            label: 'Max Time (Minutes)',
-            category: 'Experimental',
-            requiresRestart: true,
-            default: 3,
-            description:
-              'Maximum time for the Codebase Investigator agent (in minutes).',
-            showInDialog: false,
-          },
-          thinkingBudget: {
-            type: 'number',
-            label: 'Thinking Budget',
-            category: 'Experimental',
-            requiresRestart: true,
-            default: 8192,
-            description:
-              'The thinking budget for the Codebase Investigator agent.',
-            showInDialog: false,
-          },
-          model: {
-            type: 'string',
-            label: 'Model',
-            category: 'Experimental',
-            requiresRestart: true,
-            default: GEMINI_MODEL_ALIAS_AUTO,
-            description:
-              'The model to use for the Codebase Investigator agent.',
-            showInDialog: false,
-          },
-        },
-      },
       useOSC52Paste: {
         type: 'boolean',
         label: 'Use OSC 52 Paste',
@@ -1531,26 +1470,6 @@ const SETTINGS_SCHEMA = {
           'Use OSC 52 sequence for pasting instead of clipboardy (useful for remote sessions).',
         showInDialog: true,
       },
-      cliHelpAgentSettings: {
-        type: 'object',
-        label: 'CLI Help Agent Settings',
-        category: 'Experimental',
-        requiresRestart: true,
-        default: {},
-        description: 'Configuration for CLI Help Agent.',
-        showInDialog: false,
-        properties: {
-          enabled: {
-            type: 'boolean',
-            label: 'Enable CLI Help Agent',
-            category: 'Experimental',
-            requiresRestart: true,
-            default: true,
-            description: 'Enable the CLI Help Agent.',
-            showInDialog: true,
-          },
-        },
-      },
       plan: {
         type: 'boolean',
         label: 'Plan',

packages/cli/src/config/settings_repro.test.ts

@@ -155,8 +155,12 @@ describe('Settings Repro', () => {
       experimental: {
         useModelRouter: false,
         enableSubagents: false,
-        codebaseInvestigatorSettings: {
+      },
-          enabled: true,
+      agents: {
+        overrides: {
+          codebase_investigator: {
+            enabled: true,
+          },
         },
       },
       ui: {

packages/cli/src/ui/components/SettingsDialog.test.tsx

@@ -381,7 +381,7 @@ describe('SettingsDialog', () => {
 
       await waitFor(() => {
         // Should wrap to last setting (without relying on exact bullet character)
-        expect(lastFrame()).toContain('Codebase Investigator Max Num Turns');
+        expect(lastFrame()).toContain('Hook Notifications');
       });
 
       unmount();
@@ -1213,9 +1213,7 @@ describe('SettingsDialog', () => {
       await waitFor(() => {
         expect(lastFrame()).toContain('vim');
         expect(lastFrame()).toContain('Vim Mode');
-        expect(lastFrame()).not.toContain(
+        expect(lastFrame()).not.toContain('Hook Notifications');
-          'Codebase Investigator Max Num Turns',
-        );
       });
 
       unmount();

packages/core/src/agents/codebase-investigator.test.ts

@@ -13,24 +13,24 @@ import {
   READ_FILE_TOOL_NAME,
 } from '../tools/tool-names.js';
 import { DEFAULT_GEMINI_MODEL } from '../config/models.js';
+import { makeFakeConfig } from '../test-utils/config.js';
 
 describe('CodebaseInvestigatorAgent', () => {
+  const config = makeFakeConfig();
+  const agent = CodebaseInvestigatorAgent(config);
+
   it('should have the correct agent definition', () => {
-    expect(CodebaseInvestigatorAgent.name).toBe('codebase_investigator');
+    expect(agent.name).toBe('codebase_investigator');
-    expect(CodebaseInvestigatorAgent.displayName).toBe(
+    expect(agent.displayName).toBe('Codebase Investigator Agent');
-      'Codebase Investigator Agent',
+    expect(agent.description).toBeDefined();
-    );
-    expect(CodebaseInvestigatorAgent.description).toBeDefined();
     const inputSchema =
       // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      CodebaseInvestigatorAgent.inputConfig.inputSchema as any;
+      agent.inputConfig.inputSchema as any;
     expect(inputSchema.properties['objective']).toBeDefined();
     expect(inputSchema.required).toContain('objective');
-    expect(CodebaseInvestigatorAgent.outputConfig?.outputName).toBe('report');
+    expect(agent.outputConfig?.outputName).toBe('report');
-    expect(CodebaseInvestigatorAgent.modelConfig?.model).toBe(
+    expect(agent.modelConfig?.model).toBe(DEFAULT_GEMINI_MODEL);
-      DEFAULT_GEMINI_MODEL,
+    expect(agent.toolConfig?.tools).toEqual([
-    );
-    expect(CodebaseInvestigatorAgent.toolConfig?.tools).toEqual([
       LS_TOOL_NAME,
       READ_FILE_TOOL_NAME,
       GLOB_TOOL_NAME,
@@ -44,7 +44,7 @@ describe('CodebaseInvestigatorAgent', () => {
       ExplorationTrace: ['trace'],
       RelevantLocations: [],
     };
-    const processed = CodebaseInvestigatorAgent.processOutput?.(report);
+    const processed = agent.processOutput?.(report);
     expect(processed).toBe(JSON.stringify(report, null, 2));
   });
 });

packages/core/src/agents/codebase-investigator.ts

@@ -11,8 +11,15 @@ import {
   LS_TOOL_NAME,
   READ_FILE_TOOL_NAME,
 } from '../tools/tool-names.js';
-import { DEFAULT_GEMINI_MODEL } from '../config/models.js';
+import {
+  DEFAULT_THINKING_MODE,
+  DEFAULT_GEMINI_MODEL,
+  PREVIEW_GEMINI_FLASH_MODEL,
+  isPreviewModel,
+} from '../config/models.js';
 import { z } from 'zod';
+import type { Config } from '../config/config.js';
+import { ThinkingLevel } from '@google/genai';
 
 // Define a type that matches the outputConfig schema for type safety.
 const CodebaseInvestigationReportSchema = z.object({
@@ -41,65 +48,82 @@ const CodebaseInvestigationReportSchema = z.object({
  * A Proof-of-Concept subagent specialized in analyzing codebase structure,
  * dependencies, and technologies.
  */
-export const CodebaseInvestigatorAgent: LocalAgentDefinition<
+export const CodebaseInvestigatorAgent = (
-  typeof CodebaseInvestigationReportSchema
+  config: Config,
-> = {
+): LocalAgentDefinition<typeof CodebaseInvestigationReportSchema> => {
-  name: 'codebase_investigator',
+  // Use Preview Flash model if the main model is any of the preview models.
-  kind: 'local',
+  // If the main model is not a preview model, use the default pro model.
-  displayName: 'Codebase Investigator Agent',
+  const model = isPreviewModel(config.getModel())
-  description: `The specialized tool for codebase analysis, architectural mapping, and understanding system-wide dependencies.
+    ? PREVIEW_GEMINI_FLASH_MODEL
+    : DEFAULT_GEMINI_MODEL;
+
+  return {
+    name: 'codebase_investigator',
+    kind: 'local',
+    displayName: 'Codebase Investigator Agent',
+    description: `The specialized tool for codebase analysis, architectural mapping, and understanding system-wide dependencies.
     Invoke this tool for tasks like vague requests, bug root-cause analysis, system refactoring, comprehensive feature implementation or to answer questions about the codebase that require investigation.
     It returns a structured report with key file paths, symbols, and actionable architectural insights.`,
-  inputConfig: {
+    inputConfig: {
-    inputSchema: {
+      inputSchema: {
-      type: 'object',
+        type: 'object',
-      properties: {
+        properties: {
-        objective: {
+          objective: {
-          type: 'string',
+            type: 'string',
-          description: `A comprehensive and detailed description of the user's ultimate goal.
+            description: `A comprehensive and detailed description of the user's ultimate goal.
           You must include original user's objective as well as questions and any extra context and questions you may have.`,
+          },
         },
-      },
+        required: ['objective'],
-      required: ['objective'],
-    },
-  },
-  outputConfig: {
-    outputName: 'report',
-    description: 'The final investigation report as a JSON object.',
-    schema: CodebaseInvestigationReportSchema,
-  },
-
-  // The 'output' parameter is now strongly typed as CodebaseInvestigationReportSchema
-  processOutput: (output) => JSON.stringify(output, null, 2),
-
-  modelConfig: {
-    model: DEFAULT_GEMINI_MODEL,
-    generateContentConfig: {
-      temperature: 0.1,
-      topP: 0.95,
-      thinkingConfig: {
-        includeThoughts: true,
-        thinkingBudget: -1,
       },
     },
-  },
+    outputConfig: {
+      outputName: 'report',
+      description: 'The final investigation report as a JSON object.',
+      schema: CodebaseInvestigationReportSchema,
+    },
 
-  runConfig: {
+    // The 'output' parameter is now strongly typed as CodebaseInvestigationReportSchema
-    maxTimeMinutes: 5,
+    processOutput: (output) => JSON.stringify(output, null, 2),
-    maxTurns: 15,
-  },
 
-  toolConfig: {
+    modelConfig: {
-    // Grant access only to read-only tools.
+      model,
-    tools: [LS_TOOL_NAME, READ_FILE_TOOL_NAME, GLOB_TOOL_NAME, GREP_TOOL_NAME],
+      generateContentConfig: {
-  },
+        temperature: 0.1,
+        topP: 0.95,
+        thinkingConfig: isPreviewModel(model)
+          ? {
+              includeThoughts: true,
+              thinkingLevel: ThinkingLevel.HIGH,
+            }
+          : {
+              includeThoughts: true,
+              thinkingBudget: DEFAULT_THINKING_MODE,
+            },
+      },
+    },
 
-  promptConfig: {
+    runConfig: {
-    query: `Your task is to do a deep investigation of the codebase to find all relevant files, code locations, architectural mental map and insights to solve  for the following user objective:
+      maxTimeMinutes: 3,
+      maxTurns: 10,
+    },
+
+    toolConfig: {
+      // Grant access only to read-only tools.
+      tools: [
+        LS_TOOL_NAME,
+        READ_FILE_TOOL_NAME,
+        GLOB_TOOL_NAME,
+        GREP_TOOL_NAME,
+      ],
+    },
+
+    promptConfig: {
+      query: `Your task is to do a deep investigation of the codebase to find all relevant files, code locations, architectural mental map and insights to solve  for the following user objective:
 <objective>
 \${objective}
 </objective>`,
-    systemPrompt: `You are **Codebase Investigator**, a hyper-specialized AI agent and an expert in reverse-engineering complex software projects. You are a sub-agent within a larger development system.
+      systemPrompt: `You are **Codebase Investigator**, a hyper-specialized AI agent and an expert in reverse-engineering complex software projects. You are a sub-agent within a larger development system.
 Your **SOLE PURPOSE** is to build a complete mental model of the code relevant to a given investigation. You must identify all relevant files, understand their roles, and foresee the direct architectural consequences of potential changes.
 You are a sub-agent in a larger system. Your only responsibility is to provide deep, actionable context.
 - **DO:** Find the key modules, classes, and functions that are part of the problem and its solution.
@@ -158,5 +182,6 @@ When you are finished, you **MUST** call the \`complete_task\` tool. The \`repor
 }
 \`\`\`
 `,
-  },
+    },
+  };
 };

packages/core/src/agents/registry.test.ts

@@ -14,7 +14,8 @@ import { coreEvents, CoreEvent } from '../utils/events.js';
 import { A2AClientManager } from './a2a-client-manager.js';
 import {
   DEFAULT_GEMINI_FLASH_LITE_MODEL,
-  GEMINI_MODEL_ALIAS_AUTO,
+  DEFAULT_GEMINI_MODEL,
+  DEFAULT_THINKING_MODE,
   PREVIEW_GEMINI_FLASH_MODEL,
   PREVIEW_GEMINI_MODEL,
   PREVIEW_GEMINI_MODEL_AUTO,
@@ -23,6 +24,7 @@ import * as tomlLoader from './agentLoader.js';
 import { SimpleExtensionLoader } from '../utils/extensionLoader.js';
 import type { ConfigParameters } from '../config/config.js';
 import type { ToolRegistry } from '../tools/tool-registry.js';
+import { ThinkingLevel } from '@google/genai';
 
 vi.mock('./agentLoader.js', () => ({
   loadAgentsFromDirectory: vi
@@ -127,14 +129,27 @@ describe('AgentRegistry', () => {
       );
     });
 
-    it('should use preview flash model for codebase investigator if main model is preview pro', async () => {
+    it('should use default model for codebase investigator for non-preview models', async () => {
-      const previewConfig = makeMockedConfig({
+      const previewConfig = makeMockedConfig({ model: DEFAULT_GEMINI_MODEL });
-        model: PREVIEW_GEMINI_MODEL,
+      const previewRegistry = new TestableAgentRegistry(previewConfig);
-        codebaseInvestigatorSettings: {
+
-          enabled: true,
+      await previewRegistry.initialize();
-          model: GEMINI_MODEL_ALIAS_AUTO,
+
-        },
+      const investigatorDef = previewRegistry.getDefinition(
+        'codebase_investigator',
+      ) as LocalAgentDefinition;
+      expect(investigatorDef).toBeDefined();
+      expect(investigatorDef?.modelConfig.model).toBe(DEFAULT_GEMINI_MODEL);
+      expect(
+        investigatorDef?.modelConfig.generateContentConfig?.thinkingConfig,
+      ).toStrictEqual({
+        includeThoughts: true,
+        thinkingBudget: DEFAULT_THINKING_MODE,
       });
+    });
+
+    it('should use preview flash model for codebase investigator if main model is preview pro', async () => {
+      const previewConfig = makeMockedConfig({ model: PREVIEW_GEMINI_MODEL });
       const previewRegistry = new TestableAgentRegistry(previewConfig);
 
       await previewRegistry.initialize();
@@ -146,15 +161,17 @@ describe('AgentRegistry', () => {
       expect(investigatorDef?.modelConfig.model).toBe(
         PREVIEW_GEMINI_FLASH_MODEL,
       );
+      expect(
+        investigatorDef?.modelConfig.generateContentConfig?.thinkingConfig,
+      ).toStrictEqual({
+        includeThoughts: true,
+        thinkingLevel: ThinkingLevel.HIGH,
+      });
     });
 
     it('should use preview flash model for codebase investigator if main model is preview auto', async () => {
       const previewConfig = makeMockedConfig({
         model: PREVIEW_GEMINI_MODEL_AUTO,
-        codebaseInvestigatorSettings: {
-          enabled: true,
-          model: GEMINI_MODEL_ALIAS_AUTO,
-        },
       });
       const previewRegistry = new TestableAgentRegistry(previewConfig);
 
@@ -172,9 +189,13 @@ describe('AgentRegistry', () => {
     it('should use the model from the investigator settings', async () => {
       const previewConfig = makeMockedConfig({
         model: PREVIEW_GEMINI_MODEL,
-        codebaseInvestigatorSettings: {
+        agents: {
-          enabled: true,
+          overrides: {
-          model: DEFAULT_GEMINI_FLASH_LITE_MODEL,
+            codebase_investigator: {
+              enabled: true,
+              modelConfig: { model: DEFAULT_GEMINI_FLASH_LITE_MODEL },
+            },
+          },
         },
       });
       const previewRegistry = new TestableAgentRegistry(previewConfig);
@@ -232,8 +253,12 @@ describe('AgentRegistry', () => {
     it('should NOT load TOML agents when enableAgents is false', async () => {
       const disabledConfig = makeMockedConfig({
         enableAgents: false,
-        codebaseInvestigatorSettings: { enabled: false },
+        agents: {
-        cliHelpAgentSettings: { enabled: false },
+          overrides: {
+            codebase_investigator: { enabled: false },
+            cli_help: { enabled: false },
+          },
+        },
       });
       const disabledRegistry = new TestableAgentRegistry(disabledConfig);
 
@@ -254,9 +279,13 @@ describe('AgentRegistry', () => {
       expect(registry.getDefinition('cli_help')).toBeDefined();
     });
 
-    it('should register CLI help agent if disabled', async () => {
+    it('should NOT register CLI help agent if disabled', async () => {
       const config = makeMockedConfig({
-        cliHelpAgentSettings: { enabled: false },
+        agents: {
+          overrides: {
+            cli_help: { enabled: false },
+          },
+        },
       });
       const registry = new TestableAgentRegistry(config);
 

packages/core/src/agents/registry.ts

@@ -16,13 +16,7 @@ import { A2AClientManager } from './a2a-client-manager.js';
 import { ADCHandler } from './remote-invocation.js';
 import { type z } from 'zod';
 import { debugLogger } from '../utils/debugLogger.js';
-import {
+import { isAutoModel } from '../config/models.js';
-  DEFAULT_GEMINI_MODEL,
-  GEMINI_MODEL_ALIAS_AUTO,
-  PREVIEW_GEMINI_FLASH_MODEL,
-  isPreviewModel,
-  isAutoModel,
-} from '../config/models.js';
 import {
   type ModelConfig,
   ModelConfigService,
@@ -149,68 +143,8 @@ export class AgentRegistry {
   }
 
   private loadBuiltInAgents(): void {
-    const investigatorSettings = this.config.getCodebaseInvestigatorSettings();
+    this.registerLocalAgent(CodebaseInvestigatorAgent(this.config));
-    const cliHelpSettings = this.config.getCliHelpAgentSettings();
+    this.registerLocalAgent(CliHelpAgent(this.config));
-    const agentsSettings = this.config.getAgentsSettings();
-    const agentsOverrides = agentsSettings.overrides ?? {};
-
-    // Only register the agent if it's enabled in the settings and not explicitly disabled via overrides.
-    if (
-      investigatorSettings?.enabled &&
-      agentsOverrides[CodebaseInvestigatorAgent.name]?.enabled !== false
-    ) {
-      let model;
-      const settingsModel = investigatorSettings.model;
-      // Check if the user explicitly set a model in the settings.
-      if (settingsModel && settingsModel !== GEMINI_MODEL_ALIAS_AUTO) {
-        model = settingsModel;
-      } else {
-        // Use Preview Flash model if the main model is any of the preview models
-        // If the main model is not preview model, use default pro model.
-        model = isPreviewModel(this.config.getModel())
-          ? PREVIEW_GEMINI_FLASH_MODEL
-          : DEFAULT_GEMINI_MODEL;
-      }
-
-      const agentDef = {
-        ...CodebaseInvestigatorAgent,
-        modelConfig: {
-          ...CodebaseInvestigatorAgent.modelConfig,
-          model,
-          generateContentConfig: {
-            ...CodebaseInvestigatorAgent.modelConfig.generateContentConfig,
-            thinkingConfig: {
-              ...CodebaseInvestigatorAgent.modelConfig.generateContentConfig
-                ?.thinkingConfig,
-              thinkingBudget:
-                investigatorSettings.thinkingBudget ??
-                CodebaseInvestigatorAgent.modelConfig.generateContentConfig
-                  ?.thinkingConfig?.thinkingBudget,
-            },
-          },
-        },
-        runConfig: {
-          ...CodebaseInvestigatorAgent.runConfig,
-          maxTimeMinutes:
-            investigatorSettings.maxTimeMinutes ??
-            CodebaseInvestigatorAgent.runConfig.maxTimeMinutes,
-          maxTurns:
-            investigatorSettings.maxNumTurns ??
-            CodebaseInvestigatorAgent.runConfig.maxTurns,
-        },
-      };
-      this.registerLocalAgent(agentDef);
-    }
-
-    // Register the CLI help agent if it's explicitly enabled and not explicitly disabled via overrides.
-    if (
-      cliHelpSettings.enabled &&
-      agentsOverrides[CliHelpAgent.name]?.enabled !== false
-    ) {
-      this.registerLocalAgent(CliHelpAgent(this.config));
-    }
-
-    // Register the generalist agent.
     this.registerLocalAgent(GeneralistAgent(this.config));
   }
 

packages/core/src/config/config.test.ts

@@ -941,10 +941,14 @@ describe('Server Config (config.ts)', () => {
       expect(wasReadFileToolRegistered).toBe(false);
     });
 
-    it('should register subagents as tools when codebaseInvestigatorSettings.enabled is true', async () => {
+    it('should register subagents as tools when agents.overrides.codebase_investigator.enabled is true', async () => {
       const params: ConfigParameters = {
         ...baseParams,
-        codebaseInvestigatorSettings: { enabled: true },
+        agents: {
+          overrides: {
+            codebase_investigator: { enabled: true },
+          },
+        },
       };
       const config = new Config(params);
 
@@ -991,11 +995,15 @@ describe('Server Config (config.ts)', () => {
       expect(registeredWrappers).toHaveLength(1);
     });
 
-    it('should not register subagents as tools when codebaseInvestigatorSettings.enabled is false', async () => {
+    it('should not register subagents as tools when agents are disabled', async () => {
       const params: ConfigParameters = {
         ...baseParams,
-        codebaseInvestigatorSettings: { enabled: false },
+        agents: {
-        cliHelpAgentSettings: { enabled: false },
+          overrides: {
+            codebase_investigator: { enabled: false },
+            cli_help: { enabled: false },
+          },
+        },
       };
       const config = new Config(params);
 
@@ -1010,11 +1018,6 @@ describe('Server Config (config.ts)', () => {
       expect(DelegateToAgentToolMock).not.toHaveBeenCalled();
     });
 
-    it('should not set default codebase investigator model in config (defaults in registry)', () => {
-      const config = new Config(baseParams);
-      expect(config.getCodebaseInvestigatorSettings()?.model).toBeUndefined();
-    });
-
     describe('with minified tool class names', () => {
       beforeEach(() => {
         Object.defineProperty(

packages/core/src/config/config.ts

@@ -49,7 +49,6 @@ import {
   DEFAULT_GEMINI_EMBEDDING_MODEL,
   DEFAULT_GEMINI_FLASH_MODEL,
   DEFAULT_GEMINI_MODEL_AUTO,
-  DEFAULT_THINKING_MODE,
   isPreviewModel,
   PREVIEW_GEMINI_MODEL,
   PREVIEW_GEMINI_MODEL_AUTO,
@@ -144,14 +143,6 @@ export interface OutputSettings {
   format?: OutputFormat;
 }
 
-export interface CodebaseInvestigatorSettings {
-  enabled?: boolean;
-  maxNumTurns?: number;
-  maxTimeMinutes?: number;
-  thinkingBudget?: number;
-  model?: string;
-}
-
 export interface ExtensionSetting {
   name: string;
   description: string;
@@ -168,10 +159,6 @@ export interface ResolvedExtensionSetting {
   source?: string;
 }
 
-export interface CliHelpAgentSettings {
-  enabled?: boolean;
-}
-
 export interface AgentRunConfig {
   maxTimeMinutes?: number;
   maxTurns?: number;
@@ -368,8 +355,6 @@ export interface ConfigParameters {
   policyEngineConfig?: PolicyEngineConfig;
   output?: OutputSettings;
   disableModelRouterForAuth?: AuthType[];
-  codebaseInvestigatorSettings?: CodebaseInvestigatorSettings;
-  cliHelpAgentSettings?: CliHelpAgentSettings;
   continueOnFailedApiCall?: boolean;
   retryFetchErrors?: boolean;
   enableShellOutputEfficiency?: boolean;
@@ -513,8 +498,6 @@ export class Config {
   private readonly messageBus: MessageBus;
   private readonly policyEngine: PolicyEngine;
   private readonly outputSettings: OutputSettings;
-  private readonly codebaseInvestigatorSettings: CodebaseInvestigatorSettings;
-  private readonly cliHelpAgentSettings: CliHelpAgentSettings;
   private readonly continueOnFailedApiCall: boolean;
   private readonly retryFetchErrors: boolean;
   private readonly enableShellOutputEfficiency: boolean;
@@ -688,18 +671,6 @@ export class Config {
     this.enableHooks = params.enableHooks ?? true;
     this.disabledHooks = params.disabledHooks ?? [];
 
-    this.codebaseInvestigatorSettings = {
-      enabled: params.codebaseInvestigatorSettings?.enabled ?? true,
-      maxNumTurns: params.codebaseInvestigatorSettings?.maxNumTurns ?? 10,
-      maxTimeMinutes: params.codebaseInvestigatorSettings?.maxTimeMinutes ?? 3,
-      thinkingBudget:
-        params.codebaseInvestigatorSettings?.thinkingBudget ??
-        DEFAULT_THINKING_MODE,
-      model: params.codebaseInvestigatorSettings?.model,
-    };
-    this.cliHelpAgentSettings = {
-      enabled: params.cliHelpAgentSettings?.enabled ?? true,
-    };
     this.continueOnFailedApiCall = params.continueOnFailedApiCall ?? true;
     this.enableShellOutputEfficiency =
       params.enableShellOutputEfficiency ?? true;
@@ -1895,14 +1866,6 @@ export class Config {
     return this.enableHooksUI;
   }
 
-  getCodebaseInvestigatorSettings(): CodebaseInvestigatorSettings {
-    return this.codebaseInvestigatorSettings;
-  }
-
-  getCliHelpAgentSettings(): CliHelpAgentSettings {
-    return this.cliHelpAgentSettings;
-  }
-
   async createToolRegistry(): Promise<ToolRegistry> {
     const registry = new ToolRegistry(this, this.messageBus);
 
@@ -1980,10 +1943,11 @@ export class Config {
    * Registers the DelegateToAgentTool if agents or related features are enabled.
    */
   private registerDelegateToAgentTool(registry: ToolRegistry): void {
+    const agentsOverrides = this.getAgentsSettings().overrides ?? {};
     if (
       this.isAgentsEnabled() ||
-      this.getCodebaseInvestigatorSettings().enabled ||
+      agentsOverrides['codebase_investigator']?.enabled !== false ||
-      this.getCliHelpAgentSettings().enabled
+      agentsOverrides['cli_help']?.enabled !== false
     ) {
       // Check if the delegate tool itself is allowed (if allowedTools is set)
       const allowedTools = this.getAllowedTools();

schemas/settings.schema.json

@@ -1428,51 +1428,6 @@
           "default": false,
           "type": "boolean"
         },
-        "codebaseInvestigatorSettings": {
-          "title": "Codebase Investigator Settings",
-          "description": "Configuration for Codebase Investigator.",
-          "markdownDescription": "Configuration for Codebase Investigator.\n\n- Category: `Experimental`\n- Requires restart: `yes`\n- Default: `{}`",
-          "default": {},
-          "type": "object",
-          "properties": {
-            "enabled": {
-              "title": "Enable Codebase Investigator",
-              "description": "Enable the Codebase Investigator agent.",
-              "markdownDescription": "Enable the Codebase Investigator agent.\n\n- Category: `Experimental`\n- Requires restart: `yes`\n- Default: `true`",
-              "default": true,
-              "type": "boolean"
-            },
-            "maxNumTurns": {
-              "title": "Codebase Investigator Max Num Turns",
-              "description": "Maximum number of turns for the Codebase Investigator agent.",
-              "markdownDescription": "Maximum number of turns for the Codebase Investigator agent.\n\n- Category: `Experimental`\n- Requires restart: `yes`\n- Default: `10`",
-              "default": 10,
-              "type": "number"
-            },
-            "maxTimeMinutes": {
-              "title": "Max Time (Minutes)",
-              "description": "Maximum time for the Codebase Investigator agent (in minutes).",
-              "markdownDescription": "Maximum time for the Codebase Investigator agent (in minutes).\n\n- Category: `Experimental`\n- Requires restart: `yes`\n- Default: `3`",
-              "default": 3,
-              "type": "number"
-            },
-            "thinkingBudget": {
-              "title": "Thinking Budget",
-              "description": "The thinking budget for the Codebase Investigator agent.",
-              "markdownDescription": "The thinking budget for the Codebase Investigator agent.\n\n- Category: `Experimental`\n- Requires restart: `yes`\n- Default: `8192`",
-              "default": 8192,
-              "type": "number"
-            },
-            "model": {
-              "title": "Model",
-              "description": "The model to use for the Codebase Investigator agent.",
-              "markdownDescription": "The model to use for the Codebase Investigator agent.\n\n- Category: `Experimental`\n- Requires restart: `yes`\n- Default: `auto`",
-              "default": "auto",
-              "type": "string"
-            }
-          },
-          "additionalProperties": false
-        },
         "useOSC52Paste": {
           "title": "Use OSC 52 Paste",
           "description": "Use OSC 52 sequence for pasting instead of clipboardy (useful for remote sessions).",
@@ -1480,23 +1435,6 @@
           "default": false,
           "type": "boolean"
         },
-        "cliHelpAgentSettings": {
-          "title": "CLI Help Agent Settings",
-          "description": "Configuration for CLI Help Agent.",
-          "markdownDescription": "Configuration for CLI Help Agent.\n\n- Category: `Experimental`\n- Requires restart: `yes`\n- Default: `{}`",
-          "default": {},
-          "type": "object",
-          "properties": {
-            "enabled": {
-              "title": "Enable CLI Help Agent",
-              "description": "Enable the CLI Help Agent.",
-              "markdownDescription": "Enable the CLI Help Agent.\n\n- Category: `Experimental`\n- Requires restart: `yes`\n- Default: `true`",
-              "default": true,
-              "type": "boolean"
-            }
-          },
-          "additionalProperties": false
-        },
         "plan": {
           "title": "Plan",
           "description": "Enable planning features (Plan Mode and tools).",