feat(directory_tree): add excludePatterns support & documentation (#623)

- Update documentation with directory_tree declaration
- Add excludePatterns parameter to DirectoryTreeArgsSchema
- Implement pattern exclusion in buildTree function using minimatch
- Pass excludePatterns through recursive calls
- Support both simple and glob patterns for exclusion
- Maintain consistent behavior with search_files implementation

* Add tests and fix implementation

---------

Co-authored-by: Ola Hungerford <olahungerford@gmail.com>
Co-authored-by: Adam Jones <adamj+git@anthropic.com>
Co-authored-by: Adam Jones <adamj@anthropic.com>

src/filesystem/README.md

@@ -153,6 +153,19 @@ The server's directory access control follows this flow:
   - Case-insensitive matching
   - Returns full paths to matches
 
+- **directory_tree**
+  - Get recursive JSON tree structure of directory contents
+  - Inputs:
+    - `path` (string): Starting directory
+    - `excludePatterns` (string[]): Exclude any patterns. Glob formats are supported.
+  - Returns:
+    - JSON array where each entry contains:
+      - `name` (string): File/directory name
+      - `type` ('file'|'directory'): Entry type
+      - `children` (array): Present only for directories
+        - Empty array for empty directories
+        - Omitted for files
+    
 - **get_file_info**
   - Get detailed file/directory metadata
   - Input: `path` (string)

src/filesystem/__tests__/directory-tree.test.ts

@@ -0,0 +1,147 @@
+import { describe, it, expect, beforeEach, afterEach } from '@jest/globals';
+import * as fs from 'fs/promises';
+import * as path from 'path';
+import * as os from 'os';
+
+// We need to test the buildTree function, but it's defined inside the request handler
+// So we'll extract the core logic into a testable function
+import { minimatch } from 'minimatch';
+
+interface TreeEntry {
+    name: string;
+    type: 'file' | 'directory';
+    children?: TreeEntry[];
+}
+
+async function buildTreeForTesting(currentPath: string, rootPath: string, excludePatterns: string[] = []): Promise<TreeEntry[]> {
+    const entries = await fs.readdir(currentPath, {withFileTypes: true});
+    const result: TreeEntry[] = [];
+
+    for (const entry of entries) {
+        const relativePath = path.relative(rootPath, path.join(currentPath, entry.name));
+        const shouldExclude = excludePatterns.some(pattern => {
+            if (pattern.includes('*')) {
+                return minimatch(relativePath, pattern, {dot: true});
+            }
+            // For files: match exact name or as part of path
+            // For directories: match as directory path
+            return minimatch(relativePath, pattern, {dot: true}) ||
+                   minimatch(relativePath, `**/${pattern}`, {dot: true}) ||
+                   minimatch(relativePath, `**/${pattern}/**`, {dot: true});
+        });
+        if (shouldExclude)
+            continue;
+
+        const entryData: TreeEntry = {
+            name: entry.name,
+            type: entry.isDirectory() ? 'directory' : 'file'
+        };
+
+        if (entry.isDirectory()) {
+            const subPath = path.join(currentPath, entry.name);
+            entryData.children = await buildTreeForTesting(subPath, rootPath, excludePatterns);
+        }
+
+        result.push(entryData);
+    }
+
+    return result;
+}
+
+describe('buildTree exclude patterns', () => {
+    let testDir: string;
+
+    beforeEach(async () => {
+        testDir = await fs.mkdtemp(path.join(os.tmpdir(), 'filesystem-test-'));
+        
+        // Create test directory structure
+        await fs.mkdir(path.join(testDir, 'src'));
+        await fs.mkdir(path.join(testDir, 'node_modules'));
+        await fs.mkdir(path.join(testDir, '.git'));
+        await fs.mkdir(path.join(testDir, 'nested', 'node_modules'), { recursive: true });
+        
+        // Create test files
+        await fs.writeFile(path.join(testDir, '.env'), 'SECRET=value');
+        await fs.writeFile(path.join(testDir, '.env.local'), 'LOCAL_SECRET=value');
+        await fs.writeFile(path.join(testDir, 'src', 'index.js'), 'console.log("hello");');
+        await fs.writeFile(path.join(testDir, 'package.json'), '{}');
+        await fs.writeFile(path.join(testDir, 'node_modules', 'module.js'), 'module.exports = {};');
+        await fs.writeFile(path.join(testDir, 'nested', 'node_modules', 'deep.js'), 'module.exports = {};');
+    });
+
+    afterEach(async () => {
+        await fs.rm(testDir, { recursive: true, force: true });
+    });
+
+    it('should exclude files matching simple patterns', async () => {
+        // Test the current implementation - this will fail until the bug is fixed
+        const tree = await buildTreeForTesting(testDir, testDir, ['.env']);
+        const fileNames = tree.map(entry => entry.name);
+        
+        expect(fileNames).not.toContain('.env');
+        expect(fileNames).toContain('.env.local'); // Should not exclude this
+        expect(fileNames).toContain('src');
+        expect(fileNames).toContain('package.json');
+    });
+
+    it('should exclude directories matching simple patterns', async () => {
+        const tree = await buildTreeForTesting(testDir, testDir, ['node_modules']);
+        const dirNames = tree.map(entry => entry.name);
+        
+        expect(dirNames).not.toContain('node_modules');
+        expect(dirNames).toContain('src');
+        expect(dirNames).toContain('.git');
+    });
+
+    it('should exclude nested directories with same pattern', async () => {
+        const tree = await buildTreeForTesting(testDir, testDir, ['node_modules']);
+        
+        // Find the nested directory
+        const nestedDir = tree.find(entry => entry.name === 'nested');
+        expect(nestedDir).toBeDefined();
+        expect(nestedDir!.children).toBeDefined();
+        
+        // The nested/node_modules should also be excluded
+        const nestedChildren = nestedDir!.children!.map(child => child.name);
+        expect(nestedChildren).not.toContain('node_modules');
+    });
+
+    it('should handle glob patterns correctly', async () => {
+        const tree = await buildTreeForTesting(testDir, testDir, ['*.env']);
+        const fileNames = tree.map(entry => entry.name);
+        
+        expect(fileNames).not.toContain('.env');
+        expect(fileNames).toContain('.env.local'); // *.env should not match .env.local
+        expect(fileNames).toContain('src');
+    });
+
+    it('should handle dot files correctly', async () => {
+        const tree = await buildTreeForTesting(testDir, testDir, ['.git']);
+        const dirNames = tree.map(entry => entry.name);
+        
+        expect(dirNames).not.toContain('.git');
+        expect(dirNames).toContain('.env'); // Should not exclude this
+    });
+
+    it('should work with multiple exclude patterns', async () => {
+        const tree = await buildTreeForTesting(testDir, testDir, ['node_modules', '.env', '.git']);
+        const entryNames = tree.map(entry => entry.name);
+        
+        expect(entryNames).not.toContain('node_modules');
+        expect(entryNames).not.toContain('.env');
+        expect(entryNames).not.toContain('.git');
+        expect(entryNames).toContain('src');
+        expect(entryNames).toContain('package.json');
+    });
+
+    it('should handle empty exclude patterns', async () => {
+        const tree = await buildTreeForTesting(testDir, testDir, []);
+        const entryNames = tree.map(entry => entry.name);
+        
+        // All entries should be included
+        expect(entryNames).toContain('node_modules');
+        expect(entryNames).toContain('.env');
+        expect(entryNames).toContain('.git');
+        expect(entryNames).toContain('src');
+    });
+});

src/filesystem/index.ts

@@ -14,6 +14,7 @@ import { createReadStream } from "fs";
 import path from "path";
 import { z } from "zod";
 import { zodToJsonSchema } from "zod-to-json-schema";
+import { minimatch } from "minimatch";
 import { normalizePath, expandHome } from './path-utils.js';
 import { getValidRootDirectories } from './roots-utils.js';
 import {
@@ -121,6 +122,7 @@ const ListDirectoryWithSizesArgsSchema = z.object({
 
 const DirectoryTreeArgsSchema = z.object({
   path: z.string(),
+  excludePatterns: z.array(z.string()).optional().default([])
 });
 
 const MoveFileArgsSchema = z.object({
@@ -528,13 +530,28 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
             type: 'file' | 'directory';
             children?: TreeEntry[];
         }
+        const rootPath = parsed.data.path;
 
-        async function buildTree(currentPath: string): Promise<TreeEntry[]> {
+        async function buildTree(currentPath: string, excludePatterns: string[] = []): Promise<TreeEntry[]> {
             const validPath = await validatePath(currentPath);
             const entries = await fs.readdir(validPath, {withFileTypes: true});
             const result: TreeEntry[] = [];
 
             for (const entry of entries) {
+                const relativePath = path.relative(rootPath, path.join(currentPath, entry.name));
+                const shouldExclude = excludePatterns.some(pattern => {
+                    if (pattern.includes('*')) {
+                        return minimatch(relativePath, pattern, {dot: true});
+                    }
+                    // For files: match exact name or as part of path
+                    // For directories: match as directory path
+                    return minimatch(relativePath, pattern, {dot: true}) ||
+                           minimatch(relativePath, `**/${pattern}`, {dot: true}) ||
+                           minimatch(relativePath, `**/${pattern}/**`, {dot: true});
+                });
+                if (shouldExclude)
+                    continue;
+
                 const entryData: TreeEntry = {
                     name: entry.name,
                     type: entry.isDirectory() ? 'directory' : 'file'
@@ -542,7 +559,7 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
 
                 if (entry.isDirectory()) {
                     const subPath = path.join(currentPath, entry.name);
-                    entryData.children = await buildTree(subPath);
+                    entryData.children = await buildTree(subPath, excludePatterns);
                 }
 
                 result.push(entryData);
@@ -551,7 +568,7 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
             return result;
         }
 
-        const treeData = await buildTree(parsed.data.path);
+        const treeData = await buildTree(rootPath, parsed.data.excludePatterns);
         return {
             content: [{
                 type: "text",