Merge branch 'main' into add-roots-support-to-everything-server

src/filesystem/README.md

@@ -145,14 +145,27 @@ The server's directory access control follows this flow:
   - Fails if destination exists
 
 - **search_files**
-  - Recursively search for files/directories
+  - Recursively search for files/directories that match or do not match patterns
   - Inputs:
     - `path` (string): Starting directory
     - `pattern` (string): Search pattern
-    - `excludePatterns` (string[]): Exclude any patterns. Glob formats are supported.
-  - Case-insensitive matching
+    - `excludePatterns` (string[]): Exclude any patterns.
+  - Glob-style pattern 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/__tests__/lib.test.ts

@@ -316,7 +316,7 @@ describe('Lib Functions', () => {
         
         const result = await searchFilesWithValidation(
           testDir,
-          'test',
+          '*test*',
           allowedDirs,
           { excludePatterns: ['*.log', 'node_modules'] }
         );
@@ -346,7 +346,7 @@ describe('Lib Functions', () => {
         
         const result = await searchFilesWithValidation(
           testDir,
-          'test',
+          '*test*',
           allowedDirs,
           {}
         );
@@ -370,7 +370,7 @@ describe('Lib Functions', () => {
         
         const result = await searchFilesWithValidation(
           testDir,
-          'test',
+          '*test*',
           allowedDirs,
           { excludePatterns: ['*.backup'] }
         );

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 {
@@ -87,7 +88,10 @@ const ReadMediaFileArgsSchema = z.object({
 });
 
 const ReadMultipleFilesArgsSchema = z.object({
-  paths: z.array(z.string()),
+  paths: z
+    .array(z.string())
+    .min(1, "At least one file path must be provided")
+    .describe("Array of file paths to read. Each path must be a string pointing to a valid file within allowed directories."),
 });
 
 const WriteFileArgsSchema = z.object({
@@ -121,6 +125,7 @@ const ListDirectoryWithSizesArgsSchema = z.object({
 
 const DirectoryTreeArgsSchema = z.object({
   path: z.string(),
+  excludePatterns: z.array(z.string()).optional().default([])
 });
 
 const MoveFileArgsSchema = z.object({
@@ -275,9 +280,9 @@ server.setRequestHandler(ListToolsRequestSchema, async () => {
         name: "search_files",
         description:
           "Recursively search for files and directories matching a pattern. " +
-          "Searches through all subdirectories from the starting path. The search " +
-          "is case-insensitive and matches partial names. Returns full paths to all " +
-          "matching items. Great for finding files when you don't know their exact location. " +
+          "The patterns should be glob-style patterns that match paths relative to the working directory. " +
+          "Use pattern like '*.ext' to match files in current directory, and '**/*.ext' to match files in all subdirectories. " +
+          "Returns full paths to all matching items. Great for finding files when you don't know their exact location. " +
           "Only searches within allowed directories.",
         inputSchema: zodToJsonSchema(SearchFilesArgsSchema) as ToolInput,
       },
@@ -528,13 +533,28 @@ 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 +562,7 @@ 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 +571,7 @@ 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",

src/filesystem/lib.ts

@@ -367,14 +367,14 @@ export async function searchFilesWithValidation(
         await validatePath(fullPath);
 
         const relativePath = path.relative(rootPath, fullPath);
-        const shouldExclude = excludePatterns.some(excludePattern => {
-          const globPattern = excludePattern.includes('*') ? excludePattern : `**/${excludePattern}/**`;
-          return minimatch(relativePath, globPattern, { dot: true });
-        });
+        const shouldExclude = excludePatterns.some(excludePattern =>
+          minimatch(relativePath, excludePattern, { dot: true })
+        );
 
         if (shouldExclude) continue;
 
-        if (entry.name.toLowerCase().includes(pattern.toLowerCase())) {
+        // Use glob matching for the search pattern
+        if (minimatch(relativePath, pattern, { dot: true })) {
           results.push(fullPath);
         }
 

src/git/README.md

@@ -57,10 +57,12 @@ Please note that mcp-server-git is currently in early development. The functiona
    - Returns: Confirmation of reset operation
 
 8. `git_log`
-   - Shows the commit logs
+   - Shows the commit logs with optional date filtering
    - Inputs:
      - `repo_path` (string): Path to Git repository
      - `max_count` (number, optional): Maximum number of commits to show (default: 10)
+     - `start_timestamp` (string, optional): Start timestamp for filtering commits. Accepts ISO 8601 format (e.g., '2024-01-15T14:30:25'), relative dates (e.g., '2 weeks ago', 'yesterday'), or absolute dates (e.g., '2024-01-15', 'Jan 15 2024')
+     - `end_timestamp` (string, optional): End timestamp for filtering commits. Accepts ISO 8601 format (e.g., '2024-01-15T14:30:25'), relative dates (e.g., '2 weeks ago', 'yesterday'), or absolute dates (e.g., '2024-01-15', 'Jan 15 2024')
    - Returns: Array of commit entries with hash, author, date, and message
 
 9. `git_create_branch`

src/git/src/mcp_server_git/server.py

@@ -48,6 +48,14 @@ class GitReset(BaseModel):
 class GitLog(BaseModel):
     repo_path: str
     max_count: int = 10
+    start_timestamp: Optional[str] = Field(
+        None,
+        description="Start timestamp for filtering commits. Accepts: ISO 8601 format (e.g., '2024-01-15T14:30:25'), relative dates (e.g., '2 weeks ago', 'yesterday'), or absolute dates (e.g., '2024-01-15', 'Jan 15 2024')"
+    )
+    end_timestamp: Optional[str] = Field(
+        None,
+        description="End timestamp for filtering commits. Accepts: ISO 8601 format (e.g., '2024-01-15T14:30:25'), relative dates (e.g., '2 weeks ago', 'yesterday'), or absolute dates (e.g., '2024-01-15', 'Jan 15 2024')"
+    )
 
 class GitCreateBranch(BaseModel):
     repo_path: str
@@ -83,6 +91,7 @@ class GitBranch(BaseModel):
         description="The commit sha that branch should NOT contain. Do not pass anything to this param if no commit sha is specified",
     )
 
+
 class GitTools(str, Enum):
     STATUS = "git_status"
     DIFF_UNSTAGED = "git_diff_unstaged"
@@ -125,17 +134,41 @@ def git_reset(repo: git.Repo) -> str:
     repo.index.reset()
     return "All staged changes reset"
 
-def git_log(repo: git.Repo, max_count: int = 10) -> list[str]:
-    commits = list(repo.iter_commits(max_count=max_count))
-    log = []
-    for commit in commits:
-        log.append(
-            f"Commit: {commit.hexsha!r}\n"
-            f"Author: {commit.author!r}\n"
-            f"Date: {commit.authored_datetime}\n"
-            f"Message: {commit.message!r}\n"
-        )
-    return log
+def git_log(repo: git.Repo, max_count: int = 10, start_timestamp: Optional[str] = None, end_timestamp: Optional[str] = None) -> list[str]:
+    if start_timestamp or end_timestamp:
+        # Use git log command with date filtering
+        args = []
+        if start_timestamp:
+            args.extend(['--since', start_timestamp])
+        if end_timestamp:
+            args.extend(['--until', end_timestamp])
+        args.extend(['--format=%H%n%an%n%ad%n%s%n'])
+        
+        log_output = repo.git.log(*args).split('\n')
+        
+        log = []
+        # Process commits in groups of 4 (hash, author, date, message)
+        for i in range(0, len(log_output), 4):
+            if i + 3 < len(log_output) and len(log) < max_count:
+                log.append(
+                    f"Commit: {log_output[i]}\n"
+                    f"Author: {log_output[i+1]}\n"
+                    f"Date: {log_output[i+2]}\n"
+                    f"Message: {log_output[i+3]}\n"
+                )
+        return log
+    else:
+        # Use existing logic for simple log without date filtering
+        commits = list(repo.iter_commits(max_count=max_count))
+        log = []
+        for commit in commits:
+            log.append(
+                f"Commit: {commit.hexsha!r}\n"
+                f"Author: {commit.author!r}\n"
+                f"Date: {commit.authored_datetime}\n"
+                f"Message: {commit.message!r}\n"
+            )
+        return log
 
 def git_create_branch(repo: git.Repo, branch_name: str, base_branch: str | None = None) -> str:
     if base_branch:
@@ -203,6 +236,7 @@ def git_branch(repo: git.Repo, branch_type: str, contains: str | None = None, no
 
     return branch_info
 
+
 async def serve(repository: Path | None) -> None:
     logger = logging.getLogger(__name__)
 
@@ -283,6 +317,7 @@ async def serve(repository: Path | None) -> None:
                 name=GitTools.BRANCH,
                 description="List Git branches",
                 inputSchema=GitBranch.model_json_schema(),
+
             )
         ]
 
@@ -380,13 +415,19 @@ async def serve(repository: Path | None) -> None:
                     text=result
                 )]
 
+            # Update the LOG case:
             case GitTools.LOG:
-                log = git_log(repo, arguments.get("max_count", 10))
+                log = git_log(
+                    repo, 
+                    arguments.get("max_count", 10),
+                    arguments.get("start_timestamp"),
+                    arguments.get("end_timestamp")
+                )
                 return [TextContent(
                     type="text",
                     text="Commit history:\n" + "\n".join(log)
                 )]
-
+            
             case GitTools.CREATE_BRANCH:
                 result = git_create_branch(
                     repo,
@@ -423,7 +464,7 @@ async def serve(repository: Path | None) -> None:
                     type="text",
                     text=result
                 )]
-
+            
             case _:
                 raise ValueError(f"Unknown tool: {name}")
 

src/sequentialthinking/index.ts

@@ -206,12 +206,12 @@ You should:
       },
       thoughtNumber: {
         type: "integer",
-        description: "Current thought number",
+        description: "Current thought number (numeric value, e.g., 1, 2, 3)",
         minimum: 1
       },
       totalThoughts: {
         type: "integer",
-        description: "Estimated total thoughts needed",
+        description: "Estimated total thoughts needed (numeric value, e.g., 5, 10)",
         minimum: 1
       },
       isRevision: {