@google/gemini-cli 0.7.0-nightly.20250912.68035591 → 0.7.0-preview.0

package/dist/src/config/policy.test.js

@@ -0,0 +1,336 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+import { describe, it, expect } from 'vitest';
+import { createPolicyEngineConfig } from './policy.js';
+import { ApprovalMode, PolicyDecision } from '@google/gemini-cli-core';
+describe('createPolicyEngineConfig', () => {
+    it('should return ASK_USER for all tools by default', () => {
+        const settings = {};
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        expect(config.defaultDecision).toBe(PolicyDecision.ASK_USER);
+        expect(config.rules).toEqual([
+            { toolName: 'replace', decision: 'ask_user', priority: 10 },
+            { toolName: 'save_memory', decision: 'ask_user', priority: 10 },
+            { toolName: 'run_shell_command', decision: 'ask_user', priority: 10 },
+            { toolName: 'write_file', decision: 'ask_user', priority: 10 },
+            { toolName: 'web_fetch', decision: 'ask_user', priority: 10 },
+        ]);
+    });
+    it('should allow tools in tools.allowed', () => {
+        const settings = {
+            tools: { allowed: ['run_shell_command'] },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        const rule = config.rules?.find((r) => r.toolName === 'run_shell_command' &&
+            r.decision === PolicyDecision.ALLOW);
+        expect(rule).toBeDefined();
+        expect(rule?.priority).toBe(100);
+    });
+    it('should deny tools in tools.exclude', () => {
+        const settings = {
+            tools: { exclude: ['run_shell_command'] },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        const rule = config.rules?.find((r) => r.toolName === 'run_shell_command' &&
+            r.decision === PolicyDecision.DENY);
+        expect(rule).toBeDefined();
+        expect(rule?.priority).toBe(200);
+    });
+    it('should allow tools from allowed MCP servers', () => {
+        const settings = {
+            mcp: { allowed: ['my-server'] },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        const rule = config.rules?.find((r) => r.toolName === 'my-server__*' && r.decision === PolicyDecision.ALLOW);
+        expect(rule).toBeDefined();
+        expect(rule?.priority).toBe(85);
+    });
+    it('should deny tools from excluded MCP servers', () => {
+        const settings = {
+            mcp: { excluded: ['my-server'] },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        const rule = config.rules?.find((r) => r.toolName === 'my-server__*' && r.decision === PolicyDecision.DENY);
+        expect(rule).toBeDefined();
+        expect(rule?.priority).toBe(195);
+    });
+    it('should allow tools from trusted MCP servers', () => {
+        const settings = {
+            mcpServers: {
+                'trusted-server': {
+                    command: 'node',
+                    args: ['server.js'],
+                    trust: true,
+                },
+                'untrusted-server': {
+                    command: 'node',
+                    args: ['server.js'],
+                    trust: false,
+                },
+            },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        const trustedRule = config.rules?.find((r) => r.toolName === 'trusted-server__*' &&
+            r.decision === PolicyDecision.ALLOW);
+        expect(trustedRule).toBeDefined();
+        expect(trustedRule?.priority).toBe(90);
+        // Untrusted server should not have an allow rule
+        const untrustedRule = config.rules?.find((r) => r.toolName === 'untrusted-server__*' &&
+            r.decision === PolicyDecision.ALLOW);
+        expect(untrustedRule).toBeUndefined();
+    });
+    it('should handle multiple MCP server configurations together', () => {
+        const settings = {
+            mcp: {
+                allowed: ['allowed-server'],
+                excluded: ['excluded-server'],
+            },
+            mcpServers: {
+                'trusted-server': {
+                    command: 'node',
+                    args: ['server.js'],
+                    trust: true,
+                },
+            },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        // Check allowed server
+        const allowedRule = config.rules?.find((r) => r.toolName === 'allowed-server__*' &&
+            r.decision === PolicyDecision.ALLOW);
+        expect(allowedRule).toBeDefined();
+        expect(allowedRule?.priority).toBe(85);
+        // Check trusted server
+        const trustedRule = config.rules?.find((r) => r.toolName === 'trusted-server__*' &&
+            r.decision === PolicyDecision.ALLOW);
+        expect(trustedRule).toBeDefined();
+        expect(trustedRule?.priority).toBe(90);
+        // Check excluded server
+        const excludedRule = config.rules?.find((r) => r.toolName === 'excluded-server__*' &&
+            r.decision === PolicyDecision.DENY);
+        expect(excludedRule).toBeDefined();
+        expect(excludedRule?.priority).toBe(195);
+    });
+    it('should allow read-only tools if autoAccept is true', () => {
+        const settings = {
+            tools: { autoAccept: true },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        const rule = config.rules?.find((r) => r.toolName === 'glob' && r.decision === PolicyDecision.ALLOW);
+        expect(rule).toBeDefined();
+        expect(rule?.priority).toBe(50);
+    });
+    it('should allow all tools in YOLO mode', () => {
+        const settings = {};
+        const config = createPolicyEngineConfig(settings, ApprovalMode.YOLO);
+        const rule = config.rules?.find((r) => r.decision === PolicyDecision.ALLOW && r.priority === 0);
+        expect(rule).toBeDefined();
+    });
+    it('should allow edit tool in AUTO_EDIT mode', () => {
+        const settings = {};
+        const config = createPolicyEngineConfig(settings, ApprovalMode.AUTO_EDIT);
+        const rule = config.rules?.find((r) => r.toolName === 'replace' && r.decision === PolicyDecision.ALLOW);
+        expect(rule).toBeDefined();
+        expect(rule?.priority).toBe(15);
+    });
+    it('should prioritize exclude over allow', () => {
+        const settings = {
+            tools: { allowed: ['run_shell_command'], exclude: ['run_shell_command'] },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        const denyRule = config.rules?.find((r) => r.toolName === 'run_shell_command' &&
+            r.decision === PolicyDecision.DENY);
+        const allowRule = config.rules?.find((r) => r.toolName === 'run_shell_command' &&
+            r.decision === PolicyDecision.ALLOW);
+        expect(denyRule).toBeDefined();
+        expect(allowRule).toBeDefined();
+        expect(denyRule.priority).toBeGreaterThan(allowRule.priority);
+    });
+    it('should prioritize specific tool allows over MCP server excludes', () => {
+        const settings = {
+            mcp: { excluded: ['my-server'] },
+            tools: { allowed: ['my-server__specific-tool'] },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        const serverDenyRule = config.rules?.find((r) => r.toolName === 'my-server__*' && r.decision === PolicyDecision.DENY);
+        const toolAllowRule = config.rules?.find((r) => r.toolName === 'my-server__specific-tool' &&
+            r.decision === PolicyDecision.ALLOW);
+        expect(serverDenyRule).toBeDefined();
+        expect(serverDenyRule?.priority).toBe(195);
+        expect(toolAllowRule).toBeDefined();
+        expect(toolAllowRule?.priority).toBe(100);
+        // Tool allow (100) has lower priority than server deny (195),
+        // so server deny wins - this might be counterintuitive
+    });
+    it('should prioritize specific tool excludes over MCP server allows', () => {
+        const settings = {
+            mcp: { allowed: ['my-server'] },
+            mcpServers: {
+                'my-server': {
+                    command: 'node',
+                    args: ['server.js'],
+                    trust: true,
+                },
+            },
+            tools: { exclude: ['my-server__dangerous-tool'] },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        const serverAllowRule = config.rules?.find((r) => r.toolName === 'my-server__*' && r.decision === PolicyDecision.ALLOW);
+        const toolDenyRule = config.rules?.find((r) => r.toolName === 'my-server__dangerous-tool' &&
+            r.decision === PolicyDecision.DENY);
+        expect(serverAllowRule).toBeDefined();
+        expect(toolDenyRule).toBeDefined();
+        expect(toolDenyRule.priority).toBeGreaterThan(serverAllowRule.priority);
+    });
+    it('should handle complex priority scenarios correctly', () => {
+        const settings = {
+            tools: {
+                autoAccept: true, // Priority 50 for read-only tools
+                allowed: ['my-server__tool1', 'other-tool'], // Priority 100
+                exclude: ['my-server__tool2', 'glob'], // Priority 200
+            },
+            mcp: {
+                allowed: ['allowed-server'], // Priority 85
+                excluded: ['excluded-server'], // Priority 195
+            },
+            mcpServers: {
+                'trusted-server': {
+                    command: 'node',
+                    args: ['server.js'],
+                    trust: true, // Priority 90
+                },
+            },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        // Verify glob is denied even though autoAccept would allow it
+        const globDenyRule = config.rules?.find((r) => r.toolName === 'glob' && r.decision === PolicyDecision.DENY);
+        const globAllowRule = config.rules?.find((r) => r.toolName === 'glob' && r.decision === PolicyDecision.ALLOW);
+        expect(globDenyRule).toBeDefined();
+        expect(globAllowRule).toBeDefined();
+        expect(globDenyRule.priority).toBe(200);
+        expect(globAllowRule.priority).toBe(50);
+        // Verify all priority levels are correct
+        const priorities = config.rules
+            ?.map((r) => ({
+            tool: r.toolName,
+            decision: r.decision,
+            priority: r.priority,
+        }))
+            .sort((a, b) => (b.priority ?? 0) - (a.priority ?? 0));
+        // Check that the highest priority items are the excludes
+        const highestPriorityExcludes = priorities?.filter((p) => p.priority === 200);
+        expect(highestPriorityExcludes?.every((p) => p.decision === PolicyDecision.DENY)).toBe(true);
+    });
+    it('should handle MCP servers with undefined trust property', () => {
+        const settings = {
+            mcpServers: {
+                'no-trust-property': {
+                    command: 'node',
+                    args: ['server.js'],
+                    // trust property is undefined/missing
+                },
+                'explicit-false': {
+                    command: 'node',
+                    args: ['server.js'],
+                    trust: false,
+                },
+            },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        // Neither server should have an allow rule
+        const noTrustRule = config.rules?.find((r) => r.toolName === 'no-trust-property__*' &&
+            r.decision === PolicyDecision.ALLOW);
+        const explicitFalseRule = config.rules?.find((r) => r.toolName === 'explicit-false__*' &&
+            r.decision === PolicyDecision.ALLOW);
+        expect(noTrustRule).toBeUndefined();
+        expect(explicitFalseRule).toBeUndefined();
+    });
+    it('should not add write tool rules in YOLO mode', () => {
+        const settings = {
+            tools: { exclude: ['dangerous-tool'] },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.YOLO);
+        // Should have the wildcard allow rule with priority 0
+        const wildcardRule = config.rules?.find((r) => !r.toolName && r.decision === PolicyDecision.ALLOW && r.priority === 0);
+        expect(wildcardRule).toBeDefined();
+        // Should NOT have any write tool rules (which would have priority 10)
+        const writeToolRules = config.rules?.filter((r) => [
+            'replace',
+            'save_memory',
+            'run_shell_command',
+            'write_file',
+            'web_fetch',
+        ].includes(r.toolName || '') && r.decision === PolicyDecision.ASK_USER);
+        expect(writeToolRules).toHaveLength(0);
+        // Should still have the exclude rule
+        const excludeRule = config.rules?.find((r) => r.toolName === 'dangerous-tool' && r.decision === PolicyDecision.DENY);
+        expect(excludeRule).toBeDefined();
+        expect(excludeRule?.priority).toBe(200);
+    });
+    it('should handle combination of trusted server and excluded server for same name', () => {
+        const settings = {
+            mcpServers: {
+                'conflicted-server': {
+                    command: 'node',
+                    args: ['server.js'],
+                    trust: true, // Priority 90
+                },
+            },
+            mcp: {
+                excluded: ['conflicted-server'], // Priority 195
+            },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        // Both rules should exist
+        const trustRule = config.rules?.find((r) => r.toolName === 'conflicted-server__*' &&
+            r.decision === PolicyDecision.ALLOW);
+        const excludeRule = config.rules?.find((r) => r.toolName === 'conflicted-server__*' &&
+            r.decision === PolicyDecision.DENY);
+        expect(trustRule).toBeDefined();
+        expect(trustRule?.priority).toBe(90);
+        expect(excludeRule).toBeDefined();
+        expect(excludeRule?.priority).toBe(195);
+        // Exclude (195) should win over trust (90) when evaluated
+    });
+    it('should create all read-only tool rules when autoAccept is enabled', () => {
+        const settings = {
+            tools: { autoAccept: true },
+        };
+        const config = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        // All read-only tools should have allow rules
+        const readOnlyTools = [
+            'glob',
+            'search_file_content',
+            'list_directory',
+            'read_file',
+            'read_many_files',
+        ];
+        for (const tool of readOnlyTools) {
+            const rule = config.rules?.find((r) => r.toolName === tool && r.decision === PolicyDecision.ALLOW);
+            expect(rule).toBeDefined();
+            expect(rule?.priority).toBe(50);
+        }
+    });
+    it('should handle all approval modes correctly', () => {
+        const settings = {};
+        // Test DEFAULT mode
+        const defaultConfig = createPolicyEngineConfig(settings, ApprovalMode.DEFAULT);
+        expect(defaultConfig.defaultDecision).toBe(PolicyDecision.ASK_USER);
+        expect(defaultConfig.rules?.find((r) => !r.toolName && r.decision === PolicyDecision.ALLOW)).toBeUndefined();
+        // Test YOLO mode
+        const yoloConfig = createPolicyEngineConfig(settings, ApprovalMode.YOLO);
+        expect(yoloConfig.defaultDecision).toBe(PolicyDecision.ASK_USER);
+        const yoloWildcard = yoloConfig.rules?.find((r) => !r.toolName && r.decision === PolicyDecision.ALLOW);
+        expect(yoloWildcard).toBeDefined();
+        expect(yoloWildcard?.priority).toBe(0);
+        // Test AUTO_EDIT mode
+        const autoEditConfig = createPolicyEngineConfig(settings, ApprovalMode.AUTO_EDIT);
+        expect(autoEditConfig.defaultDecision).toBe(PolicyDecision.ASK_USER);
+        const editRule = autoEditConfig.rules?.find((r) => r.toolName === 'replace' && r.decision === PolicyDecision.ALLOW);
+        expect(editRule).toBeDefined();
+        expect(editRule?.priority).toBe(15);
+    });
+});
+//# sourceMappingURL=policy.test.js.map

package/dist/src/config/policy.test.js.map

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package/dist/src/config/settings.d.ts

@@ -34,7 +34,9 @@ export interface SettingsError {
 }
 export interface SettingsFile {
     settings: Settings;
+    originalSettings: Settings;
     path: string;
+    rawJson?: string;
 }
 export declare function needsMigration(settings: Record<string, unknown>): boolean;
 export declare function migrateSettingsToV1(v2Settings: Record<string, unknown>): Record<string, unknown>;
@@ -59,4 +61,5 @@ export declare function loadEnvironment(settings: Settings): void;
  * Project settings override user settings.
  */
 export declare function loadSettings(workspaceDir?: string): LoadedSettings;
+export declare function migrateDeprecatedSettings(loadedSettings: LoadedSettings, workspaceDir?: string): void;
 export declare function saveSettings(settingsFile: SettingsFile): void;

package/dist/src/config/settings.js

@@ -16,6 +16,8 @@ import { isWorkspaceTrusted } from './trustedFolders.js';
 import { getSettingsSchema, } from './settingsSchema.js';
 import { resolveEnvVarsInObject } from '../utils/envVarResolver.js';
 import { customDeepMerge } from '../utils/deepMerge.js';
+import { updateSettingsFilePreservingFormat } from '../utils/commentJson.js';
+import { disableExtension } from './extension.js';
 function getMergeStrategyForPath(path) {
     let current = undefined;
     let currentSchema = getSettingsSchema();
@@ -32,7 +34,7 @@ export const SETTINGS_DIRECTORY_NAME = '.gemini';
 export const USER_SETTINGS_PATH = Storage.getGlobalSettingsPath();
 export const USER_SETTINGS_DIR = path.dirname(USER_SETTINGS_PATH);
 export const DEFAULT_EXCLUDED_ENV_VARS = ['DEBUG', 'DEBUG_MODE'];
-const MIGRATE_V2_OVERWRITE = false;
+const MIGRATE_V2_OVERWRITE = true;
 const MIGRATION_MAP = {
     accessibility: 'ui.accessibility',
     allowedTools: 'tools.allowed',
@@ -45,10 +47,12 @@ const MIGRATION_MAP = {
     coreTools: 'tools.core',
     contextFileName: 'context.fileName',
     customThemes: 'ui.customThemes',
+    customWittyPhrases: 'ui.customWittyPhrases',
     debugKeystrokeLogging: 'general.debugKeystrokeLogging',
     disableAutoUpdate: 'general.disableAutoUpdate',
     disableUpdateNag: 'general.disableUpdateNag',
     dnsResolutionOrder: 'advanced.dnsResolutionOrder',
+    enableMessageBusIntegration: 'tools.enableMessageBusIntegration',
     enablePromptCompletion: 'general.enablePromptCompletion',
     enforcedAuthType: 'security.auth.enforcedType',
     excludeTools: 'tools.exclude',
@@ -83,7 +87,7 @@ const MIGRATION_MAP = {
     preferredEditor: 'general.preferredEditor',
     sandbox: 'tools.sandbox',
     selectedAuthType: 'security.auth.selectedType',
-    shouldUseNodePtyShell: 'tools.usePty',
+    shouldUseNodePtyShell: 'tools.shell.enableInteractiveShell',
     shellPager: 'tools.shell.pager',
     shellShowColor: 'tools.shell.showColor',
     skipNextSpeakerCheck: 'model.skipNextSpeakerCheck',
@@ -183,7 +187,20 @@ function migrateSettingsToV2(flatSettings) {
     }
     // Carry over any unrecognized keys
     for (const remainingKey of flatKeys) {
-        v2Settings[remainingKey] = flatSettings[remainingKey];
+        const existingValue = v2Settings[remainingKey];
+        const newValue = flatSettings[remainingKey];
+        if (typeof existingValue === 'object' &&
+            existingValue !== null &&
+            !Array.isArray(existingValue) &&
+            typeof newValue === 'object' &&
+            newValue !== null &&
+            !Array.isArray(newValue)) {
+            const pathAwareGetStrategy = (path) => getMergeStrategyForPath([remainingKey, ...path]);
+            v2Settings[remainingKey] = customDeepMerge(pathAwareGetStrategy, {}, newValue, existingValue);
+        }
+        else {
+            v2Settings[remainingKey] = newValue;
+        }
     }
     return v2Settings;
 }
@@ -285,6 +302,7 @@ export class LoadedSettings {
     setValue(scope, key, value) {
         const settingsFile = this.forScope(scope);
         setNestedProperty(settingsFile.settings, key, value);
+        setNestedProperty(settingsFile.originalSettings, key, value);
         this._merged = this.computeMergedSettings();
         saveSettings(settingsFile);
     }
@@ -342,7 +360,7 @@ export function setUpCloudShellEnvironment(envFilePath) {
 }
 export function loadEnvironment(settings) {
     const envFilePath = findEnvFile(process.cwd());
-    if (!isWorkspaceTrusted(settings)) {
+    if (!isWorkspaceTrusted(settings).isTrusted) {
         return;
     }
     // Cloud Shell environment variable handling
@@ -414,7 +432,7 @@ export function loadSettings(workspaceDir = process.cwd()) {
                         message: 'Settings file is not a valid JSON object.',
                         path: filePath,
                     });
-                    return {};
+                    return { settings: {} };
                 }
                 let settingsObject = rawSettings;
                 if (needsMigration(settingsObject)) {
@@ -435,7 +453,7 @@ export function loadSettings(workspaceDir = process.cwd()) {
                         settingsObject = migratedSettings;
                     }
                 }
-                return settingsObject;
+                return { settings: settingsObject, rawJson: content };
             }
         }
         catch (error) {
@@ -444,14 +462,27 @@ export function loadSettings(workspaceDir = process.cwd()) {
                 path: filePath,
             });
         }
-        return {};
+        return { settings: {} };
+    };
+    const systemResult = loadAndMigrate(systemSettingsPath, SettingScope.System);
+    const systemDefaultsResult = loadAndMigrate(systemDefaultsPath, SettingScope.SystemDefaults);
+    const userResult = loadAndMigrate(USER_SETTINGS_PATH, SettingScope.User);
+    let workspaceResult = {
+        settings: {},
+        rawJson: undefined,
     };
-    systemSettings = loadAndMigrate(systemSettingsPath, SettingScope.System);
-    systemDefaultSettings = loadAndMigrate(systemDefaultsPath, SettingScope.SystemDefaults);
-    userSettings = loadAndMigrate(USER_SETTINGS_PATH, SettingScope.User);
     if (realWorkspaceDir !== realHomeDir) {
-        workspaceSettings = loadAndMigrate(workspaceSettingsPath, SettingScope.Workspace);
-    }
+        workspaceResult = loadAndMigrate(workspaceSettingsPath, SettingScope.Workspace);
+    }
+    const systemOriginalSettings = structuredClone(systemResult.settings);
+    const systemDefaultsOriginalSettings = structuredClone(systemDefaultsResult.settings);
+    const userOriginalSettings = structuredClone(userResult.settings);
+    const workspaceOriginalSettings = structuredClone(workspaceResult.settings);
+    // Environment variables for runtime use
+    systemSettings = resolveEnvVarsInObject(systemResult.settings);
+    systemDefaultSettings = resolveEnvVarsInObject(systemDefaultsResult.settings);
+    userSettings = resolveEnvVarsInObject(userResult.settings);
+    workspaceSettings = resolveEnvVarsInObject(workspaceResult.settings);
     // Support legacy theme names
     if (userSettings.ui?.theme === 'VS') {
         userSettings.ui.theme = DefaultLight.name;
@@ -467,16 +498,12 @@ export function loadSettings(workspaceDir = process.cwd()) {
     }
     // For the initial trust check, we can only use user and system settings.
     const initialTrustCheckSettings = customDeepMerge(getMergeStrategyForPath, {}, systemSettings, userSettings);
-    const isTrusted = isWorkspaceTrusted(initialTrustCheckSettings) ?? true;
+    const isTrusted = isWorkspaceTrusted(initialTrustCheckSettings).isTrusted ?? true;
     // Create a temporary merged settings object to pass to loadEnvironment.
     const tempMergedSettings = mergeSettings(systemSettings, systemDefaultSettings, userSettings, workspaceSettings, isTrusted);
     // loadEnviroment depends on settings so we have to create a temp version of
     // the settings to avoid a cycle
     loadEnvironment(tempMergedSettings);
-    // Now that the environment is loaded, resolve variables in the settings.
-    systemSettings = resolveEnvVarsInObject(systemSettings);
-    userSettings = resolveEnvVarsInObject(userSettings);
-    workspaceSettings = resolveEnvVarsInObject(workspaceSettings);
     // Create LoadedSettings first
     if (settingsErrors.length > 0) {
         const errorMessages = settingsErrors.map((error) => `Error in ${error.path}: ${error.message}`);
@@ -485,17 +512,41 @@ export function loadSettings(workspaceDir = process.cwd()) {
     return new LoadedSettings({
         path: systemSettingsPath,
         settings: systemSettings,
+        originalSettings: systemOriginalSettings,
+        rawJson: systemResult.rawJson,
     }, {
         path: systemDefaultsPath,
         settings: systemDefaultSettings,
+        originalSettings: systemDefaultsOriginalSettings,
+        rawJson: systemDefaultsResult.rawJson,
     }, {
         path: USER_SETTINGS_PATH,
         settings: userSettings,
+        originalSettings: userOriginalSettings,
+        rawJson: userResult.rawJson,
     }, {
         path: workspaceSettingsPath,
         settings: workspaceSettings,
+        originalSettings: workspaceOriginalSettings,
+        rawJson: workspaceResult.rawJson,
     }, isTrusted, migratedInMemorScopes);
 }
+export function migrateDeprecatedSettings(loadedSettings, workspaceDir = process.cwd()) {
+    const processScope = (scope) => {
+        const settings = loadedSettings.forScope(scope).settings;
+        if (settings.extensions?.disabled) {
+            console.log(`Migrating deprecated extensions.disabled settings from ${scope} settings...`);
+            for (const extension of settings.extensions.disabled ?? []) {
+                disableExtension(extension, scope, workspaceDir);
+            }
+            const newExtensionsValue = { ...settings.extensions };
+            newExtensionsValue.disabled = undefined;
+            loadedSettings.setValue(scope, 'extensions', newExtensionsValue);
+        }
+    };
+    processScope(SettingScope.User);
+    processScope(SettingScope.Workspace);
+}
 export function saveSettings(settingsFile) {
     try {
         // Ensure the directory exists
@@ -503,11 +554,12 @@ export function saveSettings(settingsFile) {
         if (!fs.existsSync(dirPath)) {
             fs.mkdirSync(dirPath, { recursive: true });
         }
-        let settingsToSave = settingsFile.settings;
+        let settingsToSave = settingsFile.originalSettings;
         if (!MIGRATE_V2_OVERWRITE) {
             settingsToSave = migrateSettingsToV1(settingsToSave);
         }
-        fs.writeFileSync(settingsFile.path, JSON.stringify(settingsToSave, null, 2), 'utf-8');
+        // Use the format-preserving update function
+        updateSettingsFilePreservingFormat(settingsFile.path, settingsToSave);
     }
     catch (error) {
         console.error('Error saving user settings file:', error);