@office-ai/aioncli-core 0.2.2 → 0.8.1

package/dist/src/utils/memoryDiscovery.js

@@ -3,14 +3,15 @@
  * Copyright 2025 Google LLC
  * SPDX-License-Identifier: Apache-2.0
  */
-import * as fs from 'fs/promises';
-import * as fsSync from 'fs';
-import * as path from 'path';
-import { homedir } from 'os';
+import * as fs from 'node:fs/promises';
+import * as fsSync from 'node:fs';
+import * as path from 'node:path';
+import { homedir } from 'node:os';
 import { bfsFileSearch } from './bfsFileSearch.js';
-import { GEMINI_CONFIG_DIR, getAllGeminiMdFilenames, } from '../tools/memoryTool.js';
+import { getAllGeminiMdFilenames } from '../tools/memoryTool.js';
 import { processImports } from './memoryImportProcessor.js';
-import { DEFAULT_MEMORY_FILE_FILTERING_OPTIONS, } from '../config/config.js';
+import { DEFAULT_MEMORY_FILE_FILTERING_OPTIONS } from '../config/constants.js';
+import { GEMINI_DIR } from './paths.js';
 // Simple console logger, similar to the one previously in CLI's config.ts
 // TODO: Integrate with a more robust server-side logger if available/appropriate.
 const logger = {
@@ -58,24 +59,40 @@ async function findProjectRoot(startDir) {
         currentDir = parentDir;
     }
 }
-async function getGeminiMdFilePathsInternal(currentWorkingDirectory, includeDirectoriesToReadGemini, userHomePath, debugMode, fileService, extensionContextFilePaths = [], fileFilteringOptions, maxDirs) {
+async function getGeminiMdFilePathsInternal(currentWorkingDirectory, includeDirectoriesToReadGemini, userHomePath, debugMode, fileService, extensionContextFilePaths = [], folderTrust, fileFilteringOptions, maxDirs) {
     const dirs = new Set([
         ...includeDirectoriesToReadGemini,
         currentWorkingDirectory,
     ]);
-    const paths = [];
-    for (const dir of dirs) {
-        const pathsByDir = await getGeminiMdFilePathsInternalForEachDir(dir, userHomePath, debugMode, fileService, extensionContextFilePaths, fileFilteringOptions, maxDirs);
-        paths.push(...pathsByDir);
+    // Process directories in parallel with concurrency limit to prevent EMFILE errors
+    const CONCURRENT_LIMIT = 10;
+    const dirsArray = Array.from(dirs);
+    const pathsArrays = [];
+    for (let i = 0; i < dirsArray.length; i += CONCURRENT_LIMIT) {
+        const batch = dirsArray.slice(i, i + CONCURRENT_LIMIT);
+        const batchPromises = batch.map((dir) => getGeminiMdFilePathsInternalForEachDir(dir, userHomePath, debugMode, fileService, extensionContextFilePaths, folderTrust, fileFilteringOptions, maxDirs));
+        const batchResults = await Promise.allSettled(batchPromises);
+        for (const result of batchResults) {
+            if (result.status === 'fulfilled') {
+                pathsArrays.push(result.value);
+            }
+            else {
+                const error = result.reason;
+                const message = error instanceof Error ? error.message : String(error);
+                logger.error(`Error discovering files in directory: ${message}`);
+                // Continue processing other directories
+            }
+        }
     }
+    const paths = pathsArrays.flat();
     return Array.from(new Set(paths));
 }
-async function getGeminiMdFilePathsInternalForEachDir(dir, userHomePath, debugMode, fileService, extensionContextFilePaths = [], fileFilteringOptions, maxDirs) {
+async function getGeminiMdFilePathsInternalForEachDir(dir, userHomePath, debugMode, fileService, extensionContextFilePaths = [], folderTrust, fileFilteringOptions, maxDirs) {
     const allPaths = new Set();
     const geminiMdFilenames = getAllGeminiMdFilenames();
     for (const geminiMdFilename of geminiMdFilenames) {
         const resolvedHome = path.resolve(userHomePath);
-        const globalMemoryPath = path.join(resolvedHome, GEMINI_CONFIG_DIR, geminiMdFilename);
+        const globalMemoryPath = path.join(resolvedHome, GEMINI_DIR, geminiMdFilename);
         // This part that finds the global file always runs.
         try {
             await fs.access(globalMemoryPath, fsSync.constants.R_OK);
@@ -88,7 +105,7 @@ async function getGeminiMdFilePathsInternalForEachDir(dir, userHomePath, debugMo
         }
         // FIX: Only perform the workspace search (upward and downward scans)
         // if a valid currentWorkingDirectory is provided.
-        if (dir) {
+        if (dir && folderTrust) {
             const resolvedCwd = path.resolve(dir);
             if (debugMode)
                 logger.debug(`Searching for ${geminiMdFilename} starting from CWD: ${resolvedCwd}`);
@@ -101,7 +118,7 @@ async function getGeminiMdFilePathsInternalForEachDir(dir, userHomePath, debugMo
                 ? path.dirname(projectRoot)
                 : path.dirname(resolvedHome);
             while (currentDir && currentDir !== path.dirname(currentDir)) {
-                if (currentDir === path.join(resolvedHome, GEMINI_CONFIG_DIR)) {
+                if (currentDir === path.join(resolvedHome, GEMINI_DIR)) {
                     break;
                 }
                 const potentialPath = path.join(currentDir, geminiMdFilename);
@@ -147,25 +164,43 @@ async function getGeminiMdFilePathsInternalForEachDir(dir, userHomePath, debugMo
     return finalPaths;
 }
 async function readGeminiMdFiles(filePaths, debugMode, importFormat = 'tree') {
+    // Process files in parallel with concurrency limit to prevent EMFILE errors
+    const CONCURRENT_LIMIT = 20; // Higher limit for file reads as they're typically faster
     const results = [];
-    for (const filePath of filePaths) {
-        try {
-            const content = await fs.readFile(filePath, 'utf-8');
-            // Process imports in the content
-            const processedResult = await processImports(content, path.dirname(filePath), debugMode, undefined, undefined, importFormat);
-            results.push({ filePath, content: processedResult.content });
-            if (debugMode)
-                logger.debug(`Successfully read and processed imports: ${filePath} (Length: ${processedResult.content.length})`);
-        }
-        catch (error) {
-            const isTestEnv = process.env['NODE_ENV'] === 'test' || process.env['VITEST'];
-            if (!isTestEnv) {
+    for (let i = 0; i < filePaths.length; i += CONCURRENT_LIMIT) {
+        const batch = filePaths.slice(i, i + CONCURRENT_LIMIT);
+        const batchPromises = batch.map(async (filePath) => {
+            try {
+                const content = await fs.readFile(filePath, 'utf-8');
+                // Process imports in the content
+                const processedResult = await processImports(content, path.dirname(filePath), debugMode, undefined, undefined, importFormat);
+                if (debugMode)
+                    logger.debug(`Successfully read and processed imports: ${filePath} (Length: ${processedResult.content.length})`);
+                return { filePath, content: processedResult.content };
+            }
+            catch (error) {
+                const isTestEnv = process.env['NODE_ENV'] === 'test' || process.env['VITEST'];
+                if (!isTestEnv) {
+                    const message = error instanceof Error ? error.message : String(error);
+                    logger.warn(`Warning: Could not read ${getAllGeminiMdFilenames()} file at ${filePath}. Error: ${message}`);
+                }
+                if (debugMode)
+                    logger.debug(`Failed to read: ${filePath}`);
+                return { filePath, content: null }; // Still include it with null content
+            }
+        });
+        const batchResults = await Promise.allSettled(batchPromises);
+        for (const result of batchResults) {
+            if (result.status === 'fulfilled') {
+                results.push(result.value);
+            }
+            else {
+                // This case shouldn't happen since we catch all errors above,
+                // but handle it for completeness
+                const error = result.reason;
                 const message = error instanceof Error ? error.message : String(error);
-                logger.warn(`Warning: Could not read ${getAllGeminiMdFilenames()} file at ${filePath}. Error: ${message}`);
+                logger.error(`Unexpected error processing file: ${message}`);
             }
-            results.push({ filePath, content: null }); // Still include it with null content
-            if (debugMode)
-                logger.debug(`Failed to read: ${filePath}`);
         }
     }
     return results;
@@ -192,13 +227,13 @@ currentWorkingDirectoryForDisplay) {
  * Loads hierarchical GEMINI.md files and concatenates their content.
  * This function is intended for use by the server.
  */
-export async function loadServerHierarchicalMemory(currentWorkingDirectory, includeDirectoriesToReadGemini, debugMode, fileService, extensionContextFilePaths = [], importFormat = 'tree', fileFilteringOptions, maxDirs = 200) {
+export async function loadServerHierarchicalMemory(currentWorkingDirectory, includeDirectoriesToReadGemini, debugMode, fileService, extensionContextFilePaths = [], folderTrust, importFormat = 'tree', fileFilteringOptions, maxDirs = 200) {
     if (debugMode)
         logger.debug(`Loading server hierarchical memory for CWD: ${currentWorkingDirectory} (importFormat: ${importFormat})`);
     // For the server, homedir() refers to the server process's home.
     // This is consistent with how MemoryTool already finds the global path.
     const userHomePath = homedir();
-    const filePaths = await getGeminiMdFilePathsInternal(currentWorkingDirectory, includeDirectoriesToReadGemini, userHomePath, debugMode, fileService, extensionContextFilePaths, fileFilteringOptions || DEFAULT_MEMORY_FILE_FILTERING_OPTIONS, maxDirs);
+    const filePaths = await getGeminiMdFilePathsInternal(currentWorkingDirectory, includeDirectoriesToReadGemini, userHomePath, debugMode, fileService, extensionContextFilePaths, folderTrust, fileFilteringOptions || DEFAULT_MEMORY_FILE_FILTERING_OPTIONS, maxDirs);
     if (filePaths.length === 0) {
         if (debugMode)
             logger.debug('No GEMINI.md files found in hierarchy of the workspace.');

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package/dist/src/utils/memoryDiscovery.test.js

@@ -4,12 +4,13 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 import { vi, describe, it, expect, beforeEach, afterEach } from 'vitest';
-import * as fsPromises from 'fs/promises';
-import * as os from 'os';
-import * as path from 'path';
+import * as fsPromises from 'node:fs/promises';
+import * as os from 'node:os';
+import * as path from 'node:path';
 import { loadServerHierarchicalMemory } from './memoryDiscovery.js';
-import { GEMINI_CONFIG_DIR, setGeminiMdFilename, DEFAULT_CONTEXT_FILENAME, } from '../tools/memoryTool.js';
+import { setGeminiMdFilename, DEFAULT_CONTEXT_FILENAME, } from '../tools/memoryTool.js';
 import { FileDiscoveryService } from '../services/fileDiscoveryService.js';
+import { GEMINI_DIR } from './paths.js';
 vi.mock('os', async (importOriginal) => {
     const actualOs = await importOriginal();
     return {
@@ -18,6 +19,7 @@ vi.mock('os', async (importOriginal) => {
     };
 });
 describe('loadServerHierarchicalMemory', () => {
+    const DEFAULT_FOLDER_TRUST = true;
     let testRootDir;
     let cwd;
     let projectRoot;
@@ -47,18 +49,41 @@ describe('loadServerHierarchicalMemory', () => {
         // Some tests set this to a different value.
         setGeminiMdFilename(DEFAULT_CONTEXT_FILENAME);
         // Clean up the temporary directory to prevent resource leaks.
-        await fsPromises.rm(testRootDir, { recursive: true, force: true });
+        // Use maxRetries option for robust cleanup without race conditions
+        await fsPromises.rm(testRootDir, {
+            recursive: true,
+            force: true,
+            maxRetries: 3,
+            retryDelay: 10,
+        });
+    });
+    describe('when untrusted', () => {
+        it('does not load context files from untrusted workspaces', async () => {
+            await createTestFile(path.join(projectRoot, DEFAULT_CONTEXT_FILENAME), 'Project root memory');
+            await createTestFile(path.join(cwd, DEFAULT_CONTEXT_FILENAME), 'Src directory memory');
+            const { fileCount } = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], false);
+            expect(fileCount).toEqual(0);
+        });
+        it('loads context from outside the untrusted workspace', async () => {
+            await createTestFile(path.join(projectRoot, DEFAULT_CONTEXT_FILENAME), 'Project root memory'); // Untrusted
+            await createTestFile(path.join(cwd, DEFAULT_CONTEXT_FILENAME), 'Src directory memory'); // Untrusted
+            const filepath = path.join(homedir, GEMINI_DIR, DEFAULT_CONTEXT_FILENAME);
+            await createTestFile(filepath, 'default context content'); // In user home dir (outside untrusted space).
+            const { fileCount, memoryContent } = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], false);
+            expect(fileCount).toEqual(1);
+            expect(memoryContent).toContain(path.relative(cwd, filepath).toString());
+        });
     });
     it('should return empty memory and count if no context files are found', async () => {
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot));
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: '',
             fileCount: 0,
         });
     });
     it('should load only the global context file if present and others are not (default filename)', async () => {
-        const defaultContextFile = await createTestFile(path.join(homedir, GEMINI_CONFIG_DIR, DEFAULT_CONTEXT_FILENAME), 'default context content');
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot));
+        const defaultContextFile = await createTestFile(path.join(homedir, GEMINI_DIR, DEFAULT_CONTEXT_FILENAME), 'default context content');
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: `--- Context from: ${path.relative(cwd, defaultContextFile)} ---\ndefault context content\n--- End of Context from: ${path.relative(cwd, defaultContextFile)} ---`,
             fileCount: 1,
@@ -67,8 +92,8 @@ describe('loadServerHierarchicalMemory', () => {
     it('should load only the global custom context file if present and filename is changed', async () => {
         const customFilename = 'CUSTOM_AGENTS.md';
         setGeminiMdFilename(customFilename);
-        const customContextFile = await createTestFile(path.join(homedir, GEMINI_CONFIG_DIR, customFilename), 'custom context content');
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot));
+        const customContextFile = await createTestFile(path.join(homedir, GEMINI_DIR, customFilename), 'custom context content');
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: `--- Context from: ${path.relative(cwd, customContextFile)} ---\ncustom context content\n--- End of Context from: ${path.relative(cwd, customContextFile)} ---`,
             fileCount: 1,
@@ -79,7 +104,7 @@ describe('loadServerHierarchicalMemory', () => {
         setGeminiMdFilename(customFilename);
         const projectContextFile = await createTestFile(path.join(projectRoot, customFilename), 'project context content');
         const cwdContextFile = await createTestFile(path.join(cwd, customFilename), 'cwd context content');
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot));
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: `--- Context from: ${path.relative(cwd, projectContextFile)} ---\nproject context content\n--- End of Context from: ${path.relative(cwd, projectContextFile)} ---\n\n--- Context from: ${path.relative(cwd, cwdContextFile)} ---\ncwd context content\n--- End of Context from: ${path.relative(cwd, cwdContextFile)} ---`,
             fileCount: 2,
@@ -90,7 +115,7 @@ describe('loadServerHierarchicalMemory', () => {
         setGeminiMdFilename(customFilename);
         await createTestFile(path.join(cwd, 'subdir', customFilename), 'Subdir custom memory');
         await createTestFile(path.join(cwd, customFilename), 'CWD custom memory');
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot));
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: `--- Context from: ${customFilename} ---\nCWD custom memory\n--- End of Context from: ${customFilename} ---\n\n--- Context from: ${path.join('subdir', customFilename)} ---\nSubdir custom memory\n--- End of Context from: ${path.join('subdir', customFilename)} ---`,
             fileCount: 2,
@@ -99,7 +124,7 @@ describe('loadServerHierarchicalMemory', () => {
     it('should load ORIGINAL_GEMINI_MD_FILENAME files by upward traversal from CWD to project root', async () => {
         const projectRootGeminiFile = await createTestFile(path.join(projectRoot, DEFAULT_CONTEXT_FILENAME), 'Project root memory');
         const srcGeminiFile = await createTestFile(path.join(cwd, DEFAULT_CONTEXT_FILENAME), 'Src directory memory');
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot));
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: `--- Context from: ${path.relative(cwd, projectRootGeminiFile)} ---\nProject root memory\n--- End of Context from: ${path.relative(cwd, projectRootGeminiFile)} ---\n\n--- Context from: ${path.relative(cwd, srcGeminiFile)} ---\nSrc directory memory\n--- End of Context from: ${path.relative(cwd, srcGeminiFile)} ---`,
             fileCount: 2,
@@ -108,19 +133,19 @@ describe('loadServerHierarchicalMemory', () => {
     it('should load ORIGINAL_GEMINI_MD_FILENAME files by downward traversal from CWD', async () => {
         await createTestFile(path.join(cwd, 'subdir', DEFAULT_CONTEXT_FILENAME), 'Subdir memory');
         await createTestFile(path.join(cwd, DEFAULT_CONTEXT_FILENAME), 'CWD memory');
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot));
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: `--- Context from: ${DEFAULT_CONTEXT_FILENAME} ---\nCWD memory\n--- End of Context from: ${DEFAULT_CONTEXT_FILENAME} ---\n\n--- Context from: ${path.join('subdir', DEFAULT_CONTEXT_FILENAME)} ---\nSubdir memory\n--- End of Context from: ${path.join('subdir', DEFAULT_CONTEXT_FILENAME)} ---`,
             fileCount: 2,
         });
     });
     it('should load and correctly order global, upward, and downward ORIGINAL_GEMINI_MD_FILENAME files', async () => {
-        const defaultContextFile = await createTestFile(path.join(homedir, GEMINI_CONFIG_DIR, DEFAULT_CONTEXT_FILENAME), 'default context content');
+        const defaultContextFile = await createTestFile(path.join(homedir, GEMINI_DIR, DEFAULT_CONTEXT_FILENAME), 'default context content');
         const rootGeminiFile = await createTestFile(path.join(testRootDir, DEFAULT_CONTEXT_FILENAME), 'Project parent memory');
         const projectRootGeminiFile = await createTestFile(path.join(projectRoot, DEFAULT_CONTEXT_FILENAME), 'Project root memory');
         const cwdGeminiFile = await createTestFile(path.join(cwd, DEFAULT_CONTEXT_FILENAME), 'CWD memory');
         const subDirGeminiFile = await createTestFile(path.join(cwd, 'sub', DEFAULT_CONTEXT_FILENAME), 'Subdir memory');
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot));
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: `--- Context from: ${path.relative(cwd, defaultContextFile)} ---\ndefault context content\n--- End of Context from: ${path.relative(cwd, defaultContextFile)} ---\n\n--- Context from: ${path.relative(cwd, rootGeminiFile)} ---\nProject parent memory\n--- End of Context from: ${path.relative(cwd, rootGeminiFile)} ---\n\n--- Context from: ${path.relative(cwd, projectRootGeminiFile)} ---\nProject root memory\n--- End of Context from: ${path.relative(cwd, projectRootGeminiFile)} ---\n\n--- Context from: ${path.relative(cwd, cwdGeminiFile)} ---\nCWD memory\n--- End of Context from: ${path.relative(cwd, cwdGeminiFile)} ---\n\n--- Context from: ${path.relative(cwd, subDirGeminiFile)} ---\nSubdir memory\n--- End of Context from: ${path.relative(cwd, subDirGeminiFile)} ---`,
             fileCount: 5,
@@ -131,7 +156,7 @@ describe('loadServerHierarchicalMemory', () => {
         await createTestFile(path.join(projectRoot, '.gitignore'), 'node_modules');
         await createTestFile(path.join(cwd, 'node_modules', DEFAULT_CONTEXT_FILENAME), 'Ignored memory');
         const regularSubDirGeminiFile = await createTestFile(path.join(cwd, 'my_code', DEFAULT_CONTEXT_FILENAME), 'My code memory');
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], 'tree', {
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST, 'tree', {
             respectGitIgnore: true,
             respectGeminiIgnore: true,
         }, 200);
@@ -144,18 +169,18 @@ describe('loadServerHierarchicalMemory', () => {
         const consoleDebugSpy = vi
             .spyOn(console, 'debug')
             .mockImplementation(() => { });
-        for (let i = 0; i < 100; i++) {
-            await createEmptyDir(path.join(cwd, `deep_dir_${i}`));
-        }
+        // Create directories in parallel for better performance
+        const dirPromises = Array.from({ length: 2 }, (_, i) => createEmptyDir(path.join(cwd, `deep_dir_${i}`)));
+        await Promise.all(dirPromises);
         // Pass the custom limit directly to the function
-        await loadServerHierarchicalMemory(cwd, [], true, new FileDiscoveryService(projectRoot), [], 'tree', // importFormat
+        await loadServerHierarchicalMemory(cwd, [], true, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST, 'tree', // importFormat
         {
             respectGitIgnore: true,
             respectGeminiIgnore: true,
-        }, 50);
-        expect(consoleDebugSpy).toHaveBeenCalledWith(expect.stringContaining('[DEBUG] [BfsFileSearch]'), expect.stringContaining('Scanning [50/50]:'));
+        }, 1);
+        expect(consoleDebugSpy).toHaveBeenCalledWith(expect.stringContaining('[DEBUG] [BfsFileSearch]'), expect.stringContaining('Scanning [1/1]:'));
         vi.mocked(console.debug).mockRestore();
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot));
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: '',
             fileCount: 0,
@@ -163,7 +188,7 @@ describe('loadServerHierarchicalMemory', () => {
     });
     it('should load extension context file paths', async () => {
         const extensionFilePath = await createTestFile(path.join(testRootDir, 'extensions/ext1/GEMINI.md'), 'Extension memory content');
-        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [extensionFilePath]);
+        const result = await loadServerHierarchicalMemory(cwd, [], false, new FileDiscoveryService(projectRoot), [extensionFilePath], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: `--- Context from: ${path.relative(cwd, extensionFilePath)} ---\nExtension memory content\n--- End of Context from: ${path.relative(cwd, extensionFilePath)} ---`,
             fileCount: 1,
@@ -172,11 +197,48 @@ describe('loadServerHierarchicalMemory', () => {
     it('should load memory from included directories', async () => {
         const includedDir = await createEmptyDir(path.join(testRootDir, 'included'));
         const includedFile = await createTestFile(path.join(includedDir, DEFAULT_CONTEXT_FILENAME), 'included directory memory');
-        const result = await loadServerHierarchicalMemory(cwd, [includedDir], false, new FileDiscoveryService(projectRoot));
+        const result = await loadServerHierarchicalMemory(cwd, [includedDir], false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
         expect(result).toEqual({
             memoryContent: `--- Context from: ${path.relative(cwd, includedFile)} ---\nincluded directory memory\n--- End of Context from: ${path.relative(cwd, includedFile)} ---`,
             fileCount: 1,
         });
     });
+    it('should handle multiple directories and files in parallel correctly', async () => {
+        // Create multiple test directories with GEMINI.md files
+        const numDirs = 5;
+        const createdFiles = [];
+        for (let i = 0; i < numDirs; i++) {
+            const dirPath = await createEmptyDir(path.join(testRootDir, `project-${i}`));
+            const filePath = await createTestFile(path.join(dirPath, DEFAULT_CONTEXT_FILENAME), `Content from project ${i}`);
+            createdFiles.push(filePath);
+        }
+        // Load memory from all directories
+        const result = await loadServerHierarchicalMemory(cwd, createdFiles.map((f) => path.dirname(f)), false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
+        // Should have loaded all files
+        expect(result.fileCount).toBe(numDirs);
+        // Content should include all project contents
+        for (let i = 0; i < numDirs; i++) {
+            expect(result.memoryContent).toContain(`Content from project ${i}`);
+        }
+    });
+    it('should preserve order and prevent duplicates when processing multiple directories', async () => {
+        // Create overlapping directory structure
+        const parentDir = await createEmptyDir(path.join(testRootDir, 'parent'));
+        const childDir = await createEmptyDir(path.join(parentDir, 'child'));
+        await createTestFile(path.join(parentDir, DEFAULT_CONTEXT_FILENAME), 'Parent content');
+        await createTestFile(path.join(childDir, DEFAULT_CONTEXT_FILENAME), 'Child content');
+        // Include both parent and child directories
+        const result = await loadServerHierarchicalMemory(parentDir, [childDir, parentDir], // Deliberately include duplicates
+        false, new FileDiscoveryService(projectRoot), [], DEFAULT_FOLDER_TRUST);
+        // Should have both files without duplicates
+        expect(result.fileCount).toBe(2);
+        expect(result.memoryContent).toContain('Parent content');
+        expect(result.memoryContent).toContain('Child content');
+        // Check that files are not duplicated
+        const parentOccurrences = (result.memoryContent.match(/Parent content/g) || []).length;
+        const childOccurrences = (result.memoryContent.match(/Child content/g) || []).length;
+        expect(parentOccurrences).toBe(1);
+        expect(childOccurrences).toBe(1);
+    });
 });
 //# sourceMappingURL=memoryDiscovery.test.js.map

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package/dist/src/utils/memoryImportProcessor.js

@@ -3,8 +3,8 @@
  * Copyright 2025 Google LLC
  * SPDX-License-Identifier: Apache-2.0
  */
-import * as fs from 'fs/promises';
-import * as path from 'path';
+import * as fs from 'node:fs/promises';
+import * as path from 'node:path';
 import { isSubpath } from './paths.js';
 import { marked } from 'marked';
 // Simple console logger for import processing
@@ -102,34 +102,27 @@ function isLetter(char) {
 function findCodeRegions(content) {
     const regions = [];
     const tokens = marked.lexer(content);
-    // Map from raw content to a queue of its start indices in the original content.
-    const rawContentIndices = new Map();
-    function walk(token) {
+    let offset = 0;
+    function walk(token, baseOffset) {
         if (token.type === 'code' || token.type === 'codespan') {
-            if (!rawContentIndices.has(token.raw)) {
-                const indices = [];
-                let lastIndex = -1;
-                while ((lastIndex = content.indexOf(token.raw, lastIndex + 1)) !== -1) {
-                    indices.push(lastIndex);
-                }
-                rawContentIndices.set(token.raw, indices);
-            }
-            const indices = rawContentIndices.get(token.raw);
-            if (indices && indices.length > 0) {
-                // Assume tokens are processed in order of appearance.
-                // Dequeue the next available index for this raw content.
-                const idx = indices.shift();
-                regions.push([idx, idx + token.raw.length]);
-            }
+            regions.push([baseOffset, baseOffset + token.raw.length]);
         }
         if ('tokens' in token && token.tokens) {
+            let childOffset = 0;
             for (const child of token.tokens) {
-                walk(child);
+                const childIndexInParent = token.raw.indexOf(child.raw, childOffset);
+                if (childIndexInParent === -1) {
+                    logger.error(`Could not find child token in parent raw content. Aborting parsing for this branch. Child raw: "${child.raw}"`);
+                    break;
+                }
+                walk(child, baseOffset + childIndexInParent);
+                childOffset = childIndexInParent + child.raw.length;
             }
         }
     }
     for (const token of tokens) {
-        walk(token);
+        walk(token, offset);
+        offset += token.raw.length;
     }
     return regions;
 }

package/dist/src/utils/memoryImportProcessor.js.map

@@ -1 +1 @@
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