@google/gemini-cli 0.1.15 → 0.1.16-nightly.250805.99ba2f64

package/README.md

@@ -142,6 +142,34 @@ Start by `cd`ing into an existing or newly-cloned repository and running `gemini
 > What security mechanisms are in place?
 ```
 
+```text
+> Provide a step-by-step dev onboarding doc for developers new to the codebase.
+```
+
+```text
+> Summarize this codebase and highlight the most interesting patterns or techniques I could learn from.
+```
+
+```text
+> Identify potential areas for improvement or refactoring in this codebase, highlighting parts that appear fragile, complex, or hard to maintain.
+```
+
+```text
+> Which parts of this codebase might be challenging to scale or debug?
+```
+
+```text
+> Generate a README section for the [module name] module explaining what it does and how to use it.
+```
+
+```text
+> What kind of error handling and logging strategies does the project use?
+```
+
+```text
+> Which tools, libraries, and dependencies are used in this project?
+```
+
 ### Work with your existing code
 
 ```text
@@ -181,3 +209,7 @@ Head over to the [Uninstall](docs/Uninstall.md) guide for uninstallation instruc
 ## Terms of Service and Privacy Notice
 
 For details on the terms of service and privacy notice applicable to your use of Gemini CLI, see the [Terms of Service and Privacy Notice](./docs/tos-privacy.md).
+
+## Security Disclosures
+
+Please see our [security disclosure process](SECURITY.md). All [security advisories](https://github.com/google-gemini/gemini-cli/security/advisories) are managed on Github.

package/dist/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@google/gemini-cli",
-    "version": "0.1.15",
+    "version": "0.1.16-nightly.250805.99ba2f64",
     "description": "Gemini CLI",
     "repository": {
         "type": "git",
@@ -25,7 +25,7 @@
         "dist"
     ],
     "config": {
-        "sandboxImageUri": "us-docker.pkg.dev/gemini-code-dev/gemini-cli/sandbox:0.1.15"
+        "sandboxImageUri": "us-docker.pkg.dev/gemini-code-dev/gemini-cli/sandbox:0.1.16-nightly.250805.99ba2f64"
     },
     "dependencies": {
         "@google/gemini-cli-core": "file:../core",

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

@@ -28,11 +28,12 @@ export interface CliArgs {
     experimentalAcp: boolean | undefined;
     extensions: string[] | undefined;
     listExtensions: boolean | undefined;
-    ideMode: boolean | undefined;
+    ideModeFeature: boolean | undefined;
     proxy: string | undefined;
+    includeDirectories: string[] | undefined;
 }
 export declare function parseArguments(): Promise<CliArgs>;
-export declare function loadHierarchicalGeminiMemory(currentWorkingDirectory: string, debugMode: boolean, fileService: FileDiscoveryService, settings: Settings, extensionContextFilePaths?: string[], fileFilteringOptions?: FileFilteringOptions): Promise<{
+export declare function loadHierarchicalGeminiMemory(currentWorkingDirectory: string, debugMode: boolean, fileService: FileDiscoveryService, settings: Settings, extensionContextFilePaths?: string[], memoryImportFormat?: 'flat' | 'tree', fileFilteringOptions?: FileFilteringOptions): Promise<{
     memoryContent: string;
     fileCount: number;
 }>;

package/dist/src/config/config.js

@@ -3,6 +3,9 @@
  * Copyright 2025 Google LLC
  * SPDX-License-Identifier: Apache-2.0
  */
+import * as fs from 'fs';
+import * as path from 'path';
+import { homedir } from 'node:os';
 import yargs from 'yargs/yargs';
 import { hideBin } from 'yargs/helpers';
 import process from 'node:process';
@@ -27,7 +30,7 @@ export async function parseArguments() {
         alias: 'm',
         type: 'string',
         description: `Model`,
-        default: process.env.GEMINI_MODEL || DEFAULT_GEMINI_MODEL,
+        default: process.env.GEMINI_MODEL,
     })
         .option('prompt', {
         alias: 'p',
@@ -130,13 +133,21 @@ export async function parseArguments() {
         type: 'boolean',
         description: 'List all available extensions and exit.',
     })
-        .option('ide-mode', {
+        .option('ide-mode-feature', {
         type: 'boolean',
         description: 'Run in IDE mode?',
     })
         .option('proxy', {
         type: 'string',
         description: 'Proxy for gemini client, like schema://user:password@host:port',
+    })
+        .option('include-directories', {
+        type: 'array',
+        string: true,
+        description: 'Additional directories to include in the workspace (comma-separated or multiple --include-directories)',
+        coerce: (dirs) => 
+        // Handle comma-separated values
+        dirs.flatMap((dir) => dir.split(',').map((d) => d.trim())),
     })
         .version(await getCliVersion()) // This will enable the --version flag based on package.json
         .alias('v', 'version')
@@ -150,29 +161,37 @@ export async function parseArguments() {
         return true;
     });
     yargsInstance.wrap(yargsInstance.terminalWidth());
-    return yargsInstance.argv;
+    const result = yargsInstance.parseSync();
+    // The import format is now only controlled by settings.memoryImportFormat
+    // We no longer accept it as a CLI argument
+    return result;
 }
 // This function is now a thin wrapper around the server's implementation.
 // It's kept in the CLI for now as App.tsx directly calls it for memory refresh.
 // TODO: Consider if App.tsx should get memory via a server call or if Config should refresh itself.
-export async function loadHierarchicalGeminiMemory(currentWorkingDirectory, debugMode, fileService, settings, extensionContextFilePaths = [], fileFilteringOptions) {
+export async function loadHierarchicalGeminiMemory(currentWorkingDirectory, debugMode, fileService, settings, extensionContextFilePaths = [], memoryImportFormat = 'tree', fileFilteringOptions) {
+    // FIX: Use real, canonical paths for a reliable comparison to handle symlinks.
+    const realCwd = fs.realpathSync(path.resolve(currentWorkingDirectory));
+    const realHome = fs.realpathSync(path.resolve(homedir()));
+    const isHomeDirectory = realCwd === realHome;
+    // If it is the home directory, pass an empty string to the core memory
+    // function to signal that it should skip the workspace search.
+    const effectiveCwd = isHomeDirectory ? '' : currentWorkingDirectory;
     if (debugMode) {
-        logger.debug(`CLI: Delegating hierarchical memory load to server for CWD: ${currentWorkingDirectory}`);
+        logger.debug(`CLI: Delegating hierarchical memory load to server for CWD: ${currentWorkingDirectory} (memoryImportFormat: ${memoryImportFormat})`);
     }
-    // Directly call the server function.
-    // The server function will use its own homedir() for the global path.
-    return loadServerHierarchicalMemory(currentWorkingDirectory, debugMode, fileService, extensionContextFilePaths, fileFilteringOptions, settings.memoryDiscoveryMaxDirs);
+    // Directly call the server function with the corrected path.
+    return loadServerHierarchicalMemory(effectiveCwd, debugMode, fileService, extensionContextFilePaths, memoryImportFormat, fileFilteringOptions, settings.memoryDiscoveryMaxDirs);
 }
 export async function loadCliConfig(settings, extensions, sessionId, argv) {
     const debugMode = argv.debug ||
-        [process.env.DEBUG, process.env.DEBUG_MODE].some((v) => v === 'true' || v === '1');
-    const ideMode = (argv.ideMode ?? settings.ideMode ?? false) &&
-        process.env.TERM_PROGRAM === 'vscode' &&
+        [process.env.DEBUG, process.env.DEBUG_MODE].some((v) => v === 'true' || v === '1') ||
+        false;
+    const memoryImportFormat = settings.memoryImportFormat || 'tree';
+    const ideMode = settings.ideMode ?? false;
+    const ideModeFeature = (argv.ideModeFeature ?? settings.ideModeFeature ?? false) &&
         !process.env.SANDBOX;
-    let ideClient;
-    if (ideMode) {
-        ideClient = new IdeClient();
-    }
+    const ideClient = IdeClient.getInstance(ideMode && ideModeFeature);
     const allExtensions = annotateActiveExtensions(extensions, argv.extensions || []);
     const activeExtensions = extensions.filter((_, i) => allExtensions[i].isActive);
     // Set the context filename in the server's memoryTool module BEFORE loading memory
@@ -193,7 +212,7 @@ export async function loadCliConfig(settings, extensions, sessionId, argv) {
         ...settings.fileFiltering,
     };
     // Call the (now wrapper) loadHierarchicalGeminiMemory which calls the server's version
-    const { memoryContent, fileCount } = await loadHierarchicalGeminiMemory(process.cwd(), debugMode, fileService, settings, extensionContextFilePaths, fileFiltering);
+    const { memoryContent, fileCount } = await loadHierarchicalGeminiMemory(process.cwd(), debugMode, fileService, settings, extensionContextFilePaths, memoryImportFormat, fileFiltering);
     let mcpServers = mergeMcpServers(settings, activeExtensions);
     const excludeTools = mergeExcludeTools(settings, activeExtensions);
     const blockedMcpServers = [];
@@ -239,6 +258,7 @@ export async function loadCliConfig(settings, extensions, sessionId, argv) {
         embeddingModel: DEFAULT_GEMINI_EMBEDDING_MODEL,
         sandbox: sandboxConfig,
         targetDir: process.cwd(),
+        includeDirectories: argv.includeDirectories,
         debugMode,
         question: argv.promptInteractive || argv.prompt || '',
         fullContext: argv.allFiles || argv.all_files || false,
@@ -282,7 +302,7 @@ export async function loadCliConfig(settings, extensions, sessionId, argv) {
         cwd: process.cwd(),
         fileDiscoveryService: fileService,
         bugCommand: settings.bugCommand,
-        model: argv.model,
+        model: argv.model || settings.model || DEFAULT_GEMINI_MODEL,
         extensionContextFilePaths,
         maxSessionTurns: settings.maxSessionTurns ?? -1,
         experimentalAcp: argv.experimentalAcp || false,
@@ -292,6 +312,7 @@ export async function loadCliConfig(settings, extensions, sessionId, argv) {
         noBrowser: !!process.env.NO_BROWSER,
         summarizeToolOutput: settings.summarizeToolOutput,
         ideMode,
+        ideModeFeature,
         ideClient,
     });
 }

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

@@ -7,6 +7,7 @@ import { MCPServerConfig, GeminiCLIExtension } from '@google/gemini-cli-core';
 export declare const EXTENSIONS_DIRECTORY_NAME: string;
 export declare const EXTENSIONS_CONFIG_FILENAME = "gemini-extension.json";
 export interface Extension {
+    path: string;
     config: ExtensionConfig;
     contextFiles: string[];
 }

package/dist/src/config/extension.js

@@ -57,6 +57,7 @@ function loadExtension(extensionDir) {
             .map((contextFileName) => path.join(extensionDir, contextFileName))
             .filter((contextFilePath) => fs.existsSync(contextFilePath));
         return {
+            path: extensionDir,
             config,
             contextFiles,
         };
@@ -82,6 +83,7 @@ export function annotateActiveExtensions(extensions, enabledExtensionNames) {
             name: extension.config.name,
             version: extension.config.version,
             isActive: true,
+            path: extension.path,
         }));
     }
     const lowerCaseEnabledExtensions = new Set(enabledExtensionNames.map((e) => e.trim().toLowerCase()));
@@ -91,6 +93,7 @@ export function annotateActiveExtensions(extensions, enabledExtensionNames) {
             name: extension.config.name,
             version: extension.config.version,
             isActive: false,
+            path: extension.path,
         }));
     }
     const notFoundNames = new Set(lowerCaseEnabledExtensions);
@@ -104,6 +107,7 @@ export function annotateActiveExtensions(extensions, enabledExtensionNames) {
             name: extension.config.name,
             version: extension.config.version,
             isActive,
+            path: extension.path,
         });
     }
     for (const requestedName of notFoundNames) {

package/dist/src/config/extension.js.map

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+{"version":3,"file":"extension.js","sourceRoot":"","sources":["../../../src/config/extension.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAGH,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AACzB,OAAO,KAAK,IAAI,MAAM,MAAM,CAAC;AAC7B,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AAEzB,MAAM,CAAC,MAAM,yBAAyB,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC;AAC5E,MAAM,CAAC,MAAM,0BAA0B,GAAG,uBAAuB,CAAC;AAgBlE,MAAM,UAAU,cAAc,CAAC,YAAoB;IACjD,MAAM,aAAa,GAAG;QACpB,GAAG,qBAAqB,CAAC,YAAY,CAAC;QACtC,GAAG,qBAAqB,CAAC,EAAE,CAAC,OAAO,EAAE,CAAC;KACvC,CAAC;IAEF,MAAM,gBAAgB,GAAG,IAAI,GAAG,EAAqB,CAAC;IACtD,KAAK,MAAM,SAAS,IAAI,aAAa,EAAE,CAAC;QACtC,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,SAAS,CAAC,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC;YACjD,gBAAgB,CAAC,GAAG,CAAC,SAAS,CAAC,MAAM,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;QACzD,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,MAAM,EAAE,CAAC,CAAC;AAC/C,CAAC;AAED,SAAS,qBAAqB,CAAC,GAAW;IACxC,MAAM,aAAa,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,yBAAyB,CAAC,CAAC;IAChE,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,aAAa,CAAC,EAAE,CAAC;QAClC,OAAO,EAAE,CAAC;IACZ,CAAC;IAED,MAAM,UAAU,GAAgB,EAAE,CAAC;IACnC,KAAK,MAAM,MAAM,IAAI,EAAE,CAAC,WAAW,CAAC,aAAa,CAAC,EAAE,CAAC;QACnD,MAAM,YAAY,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,MAAM,CAAC,CAAC;QAEtD,MAAM,SAAS,GAAG,aAAa,CAAC,YAAY,CAAC,CAAC;QAC9C,IAAI,SAAS,IAAI,IAAI,EAAE,CAAC;YACtB,UAAU,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;QAC7B,CAAC;IACH,CAAC;IACD,OAAO,UAAU,CAAC;AACpB,CAAC;AAED,SAAS,aAAa,CAAC,YAAoB;IACzC,IAAI,CAAC,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,WAAW,EAAE,EAAE,CAAC;QAC7C,OAAO,CAAC,KAAK,CACX,4BAA4B,YAAY,2BAA2B,CACpE,CAAC;QACF,OAAO,IAAI,CAAC;IACd,CAAC;IAED,MAAM,cAAc,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,0BAA0B,CAAC,CAAC;IAC3E,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,cAAc,CAAC,EAAE,CAAC;QACnC,OAAO,CAAC,KAAK,CACX,gCAAgC,YAAY,mCAAmC,cAAc,GAAG,CACjG,CAAC;QACF,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,CAAC;QACH,MAAM,aAAa,GAAG,EAAE,CAAC,YAAY,CAAC,cAAc,EAAE,OAAO,CAAC,CAAC;QAC/D,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,aAAa,CAAoB,CAAC;QAC5D,IAAI,CAAC,MAAM,CAAC,IAAI,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC;YACpC,OAAO,CAAC,KAAK,CACX,+BAA+B,cAAc,4BAA4B,CAC1E,CAAC;YACF,OAAO,IAAI,CAAC;QACd,CAAC;QAED,MAAM,YAAY,GAAG,mBAAmB,CAAC,MAAM,CAAC;aAC7C,GAAG,CAAC,CAAC,eAAe,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,eAAe,CAAC,CAAC;aAClE,MAAM,CAAC,CAAC,eAAe,EAAE,EAAE,CAAC,EAAE,CAAC,UAAU,CAAC,eAAe,CAAC,CAAC,CAAC;QAE/D,OAAO;YACL,IAAI,EAAE,YAAY;YAClB,MAAM;YACN,YAAY;SACb,CAAC;IACJ,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CACX,8CAA8C,cAAc,KAAK,CAAC,EAAE,CACrE,CAAC;QACF,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED,SAAS,mBAAmB,CAAC,MAAuB;IAClD,IAAI,CAAC,MAAM,CAAC,eAAe,EAAE,CAAC;QAC5B,OAAO,CAAC,WAAW,CAAC,CAAC;IACvB,CAAC;SAAM,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,eAAe,CAAC,EAAE,CAAC;QAClD,OAAO,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC;IAClC,CAAC;IACD,OAAO,MAAM,CAAC,eAAe,CAAC;AAChC,CAAC;AAED,MAAM,UAAU,wBAAwB,CACtC,UAAuB,EACvB,qBAA+B;IAE/B,MAAM,mBAAmB,GAAyB,EAAE,CAAC;IAErD,IAAI,qBAAqB,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvC,OAAO,UAAU,CAAC,GAAG,CAAC,CAAC,SAAS,EAAE,EAAE,CAAC,CAAC;YACpC,IAAI,EAAE,SAAS,CAAC,MAAM,CAAC,IAAI;YAC3B,OAAO,EAAE,SAAS,CAAC,MAAM,CAAC,OAAO;YACjC,QAAQ,EAAE,IAAI;YACd,IAAI,EAAE,SAAS,CAAC,IAAI;SACrB,CAAC,CAAC,CAAC;IACN,CAAC;IAED,MAAM,0BAA0B,GAAG,IAAI,GAAG,CACxC,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC,CACzD,CAAC;IAEF,IACE,0BAA0B,CAAC,IAAI,KAAK,CAAC;QACrC,0BAA0B,CAAC,GAAG,CAAC,MAAM,CAAC,EACtC,CAAC;QACD,OAAO,UAAU,CAAC,GAAG,CAAC,CAAC,SAAS,EAAE,EAAE,CAAC,CAAC;YACpC,IAAI,EAAE,SAAS,CAAC,MAAM,CAAC,IAAI;YAC3B,OAAO,EAAE,SAAS,CAAC,MAAM,CAAC,OAAO;YACjC,QAAQ,EAAE,KAAK;YACf,IAAI,EAAE,SAAS,CAAC,IAAI;SACrB,CAAC,CAAC,CAAC;IACN,CAAC;IAED,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,0BAA0B,CAAC,CAAC;IAE1D,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;QACnC,MAAM,aAAa,GAAG,SAAS,CAAC,MAAM,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC;QAC1D,MAAM,QAAQ,GAAG,0BAA0B,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC;QAE/D,IAAI,QAAQ,EAAE,CAAC;YACb,aAAa,CAAC,MAAM,CAAC,aAAa,CAAC,CAAC;QACtC,CAAC;QAED,mBAAmB,CAAC,IAAI,CAAC;YACvB,IAAI,EAAE,SAAS,CAAC,MAAM,CAAC,IAAI;YAC3B,OAAO,EAAE,SAAS,CAAC,MAAM,CAAC,OAAO;YACjC,QAAQ;YACR,IAAI,EAAE,SAAS,CAAC,IAAI;SACrB,CAAC,CAAC;IACL,CAAC;IAED,KAAK,MAAM,aAAa,IAAI,aAAa,EAAE,CAAC;QAC1C,OAAO,CAAC,KAAK,CAAC,wBAAwB,aAAa,EAAE,CAAC,CAAC;IACzD,CAAC;IAED,OAAO,mBAAmB,CAAC;AAC7B,CAAC"}

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

@@ -8,7 +8,10 @@ import { CustomTheme } from '../ui/themes/theme.js';
 export declare const SETTINGS_DIRECTORY_NAME = ".gemini";
 export declare const USER_SETTINGS_DIR: string;
 export declare const USER_SETTINGS_PATH: string;
+export declare const DEFAULT_EXCLUDED_ENV_VARS: string[];
 export declare function getSystemSettingsPath(): string;
+export declare function getWorkspaceSettingsPath(workspaceDir: string): string;
+export type DnsResolutionOrder = 'ipv4first' | 'verbatim';
 export declare enum SettingScope {
     User = "User",
     Workspace = "Workspace",
@@ -27,6 +30,7 @@ export interface Settings {
     theme?: string;
     customThemes?: Record<string, CustomTheme>;
     selectedAuthType?: AuthType;
+    useExternalAuth?: boolean;
     sandbox?: boolean | string;
     coreTools?: string[];
     excludeTools?: string[];
@@ -45,6 +49,8 @@ export interface Settings {
     bugCommand?: BugCommandSettings;
     checkpointing?: CheckpointingSettings;
     autoConfigureMaxOldSpaceSize?: boolean;
+    /** The model name to use (e.g 'gemini-9.0-pro') */
+    model?: string;
     fileFiltering?: {
         respectGitIgnore?: boolean;
         respectGeminiIgnore?: boolean;
@@ -56,8 +62,14 @@ export interface Settings {
     maxSessionTurns?: number;
     summarizeToolOutput?: Record<string, SummarizeToolOutputSettings>;
     vimMode?: boolean;
+    memoryImportFormat?: 'tree' | 'flat';
+    ideModeFeature?: boolean;
     ideMode?: boolean;
+    disableAutoUpdate?: boolean;
+    disableUpdateNag?: boolean;
     memoryDiscoveryMaxDirs?: number;
+    excludedProjectEnvVars?: string[];
+    dnsResolutionOrder?: DnsResolutionOrder;
 }
 export interface SettingsError {
     message: string;
@@ -80,7 +92,7 @@ export declare class LoadedSettings {
     setValue<K extends keyof Settings>(scope: SettingScope, key: K, value: Settings[K]): void;
 }
 export declare function setUpCloudShellEnvironment(envFilePath: string | null): void;
-export declare function loadEnvironment(): void;
+export declare function loadEnvironment(settings?: Settings): void;
 /**
  * Loads settings from user and workspace directories.
  * Project settings override user settings.

package/dist/src/config/settings.js

@@ -14,6 +14,7 @@ import { DefaultDark } from '../ui/themes/default.js';
 export const SETTINGS_DIRECTORY_NAME = '.gemini';
 export const USER_SETTINGS_DIR = path.join(homedir(), SETTINGS_DIRECTORY_NAME);
 export const USER_SETTINGS_PATH = path.join(USER_SETTINGS_DIR, 'settings.json');
+export const DEFAULT_EXCLUDED_ENV_VARS = ['DEBUG', 'DEBUG_MODE'];
 export function getSystemSettingsPath() {
     if (process.env.GEMINI_CLI_SYSTEM_SETTINGS_PATH) {
         return process.env.GEMINI_CLI_SYSTEM_SETTINGS_PATH;
@@ -28,6 +29,9 @@ export function getSystemSettingsPath() {
         return '/etc/gemini-cli/settings.json';
     }
 }
+export function getWorkspaceSettingsPath(workspaceDir) {
+    return path.join(workspaceDir, SETTINGS_DIRECTORY_NAME, 'settings.json');
+}
 export var SettingScope;
 (function (SettingScope) {
     SettingScope["User"] = "User";
@@ -174,13 +178,51 @@ export function setUpCloudShellEnvironment(envFilePath) {
         process.env.GOOGLE_CLOUD_PROJECT = 'cloudshell-gca';
     }
 }
-export function loadEnvironment() {
+export function loadEnvironment(settings) {
     const envFilePath = findEnvFile(process.cwd());
+    // Cloud Shell environment variable handling
     if (process.env.CLOUD_SHELL === 'true') {
         setUpCloudShellEnvironment(envFilePath);
     }
+    // If no settings provided, try to load workspace settings for exclusions
+    let resolvedSettings = settings;
+    if (!resolvedSettings) {
+        const workspaceSettingsPath = getWorkspaceSettingsPath(process.cwd());
+        try {
+            if (fs.existsSync(workspaceSettingsPath)) {
+                const workspaceContent = fs.readFileSync(workspaceSettingsPath, 'utf-8');
+                const parsedWorkspaceSettings = JSON.parse(stripJsonComments(workspaceContent));
+                resolvedSettings = resolveEnvVarsInObject(parsedWorkspaceSettings);
+            }
+        }
+        catch (_e) {
+            // Ignore errors loading workspace settings
+        }
+    }
     if (envFilePath) {
-        dotenv.config({ path: envFilePath, quiet: true });
+        // Manually parse and load environment variables to handle exclusions correctly.
+        // This avoids modifying environment variables that were already set from the shell.
+        try {
+            const envFileContent = fs.readFileSync(envFilePath, 'utf-8');
+            const parsedEnv = dotenv.parse(envFileContent);
+            const excludedVars = resolvedSettings?.excludedProjectEnvVars || DEFAULT_EXCLUDED_ENV_VARS;
+            const isProjectEnvFile = !envFilePath.includes(GEMINI_DIR);
+            for (const key in parsedEnv) {
+                if (Object.hasOwn(parsedEnv, key)) {
+                    // If it's a project .env file, skip loading excluded variables.
+                    if (isProjectEnvFile && excludedVars.includes(key)) {
+                        continue;
+                    }
+                    // Load variable only if it's not already set in the environment.
+                    if (!Object.hasOwn(process.env, key)) {
+                        process.env[key] = parsedEnv[key];
+                    }
+                }
+            }
+        }
+        catch (_e) {
+            // Errors are ignored to match the behavior of `dotenv.config({ quiet: true })`.
+        }
     }
 }
 /**
@@ -188,12 +230,25 @@ export function loadEnvironment() {
  * Project settings override user settings.
  */
 export function loadSettings(workspaceDir) {
-    loadEnvironment();
     let systemSettings = {};
     let userSettings = {};
     let workspaceSettings = {};
     const settingsErrors = [];
     const systemSettingsPath = getSystemSettingsPath();
+    // FIX: Resolve paths to their canonical representation to handle symlinks
+    const resolvedWorkspaceDir = path.resolve(workspaceDir);
+    const resolvedHomeDir = path.resolve(homedir());
+    let realWorkspaceDir = resolvedWorkspaceDir;
+    try {
+        // fs.realpathSync gets the "true" path, resolving any symlinks
+        realWorkspaceDir = fs.realpathSync(resolvedWorkspaceDir);
+    }
+    catch (_e) {
+        // This is okay. The path might not exist yet, and that's a valid state.
+    }
+    // We expect homedir to always exist and be resolvable.
+    const realHomeDir = fs.realpathSync(resolvedHomeDir);
+    const workspaceSettingsPath = getWorkspaceSettingsPath(workspaceDir);
     // Load system settings
     try {
         if (fs.existsSync(systemSettingsPath)) {
@@ -229,29 +284,32 @@ export function loadSettings(workspaceDir) {
             path: USER_SETTINGS_PATH,
         });
     }
-    const workspaceSettingsPath = path.join(workspaceDir, SETTINGS_DIRECTORY_NAME, 'settings.json');
-    // Load workspace settings
-    try {
-        if (fs.existsSync(workspaceSettingsPath)) {
-            const projectContent = fs.readFileSync(workspaceSettingsPath, 'utf-8');
-            const parsedWorkspaceSettings = JSON.parse(stripJsonComments(projectContent));
-            workspaceSettings = resolveEnvVarsInObject(parsedWorkspaceSettings);
-            if (workspaceSettings.theme && workspaceSettings.theme === 'VS') {
-                workspaceSettings.theme = DefaultLight.name;
-            }
-            else if (workspaceSettings.theme &&
-                workspaceSettings.theme === 'VS2015') {
-                workspaceSettings.theme = DefaultDark.name;
+    // This comparison is now much more reliable.
+    if (realWorkspaceDir !== realHomeDir) {
+        // Load workspace settings
+        try {
+            if (fs.existsSync(workspaceSettingsPath)) {
+                const projectContent = fs.readFileSync(workspaceSettingsPath, 'utf-8');
+                const parsedWorkspaceSettings = JSON.parse(stripJsonComments(projectContent));
+                workspaceSettings = resolveEnvVarsInObject(parsedWorkspaceSettings);
+                if (workspaceSettings.theme && workspaceSettings.theme === 'VS') {
+                    workspaceSettings.theme = DefaultLight.name;
+                }
+                else if (workspaceSettings.theme &&
+                    workspaceSettings.theme === 'VS2015') {
+                    workspaceSettings.theme = DefaultDark.name;
+                }
             }
         }
+        catch (error) {
+            settingsErrors.push({
+                message: getErrorMessage(error),
+                path: workspaceSettingsPath,
+            });
+        }
     }
-    catch (error) {
-        settingsErrors.push({
-            message: getErrorMessage(error),
-            path: workspaceSettingsPath,
-        });
-    }
-    return new LoadedSettings({
+    // Create LoadedSettings first
+    const loadedSettings = new LoadedSettings({
         path: systemSettingsPath,
         settings: systemSettings,
     }, {
@@ -261,6 +319,9 @@ export function loadSettings(workspaceDir) {
         path: workspaceSettingsPath,
         settings: workspaceSettings,
     }, settingsErrors);
+    // Load environment with merged settings
+    loadEnvironment(loadedSettings.merged);
+    return loadedSettings;
 }
 export function saveSettings(settingsFile) {
     try {

package/dist/src/config/settings.js.map

@@ -1 +1 @@
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package/dist/src/gemini.d.ts

@@ -3,5 +3,7 @@
  * Copyright 2025 Google LLC
  * SPDX-License-Identifier: Apache-2.0
  */
+import { DnsResolutionOrder } from './config/settings.js';
+export declare function validateDnsResolutionOrder(order: string | undefined): DnsResolutionOrder;
 export declare function setupUnhandledRejectionHandler(): void;
 export declare function main(): Promise<void>;