Automatic update of packages

.github/dependabot.yml

@@ -1,6 +0,0 @@
-version: 2
-updates:
-  - package-ecosystem: 'github-actions'
-    directory: '/'
-    schedule:
-      interval: 'weekly'

.github/workflows/python.yml

@@ -36,10 +36,10 @@ jobs:
       - uses: actions/checkout@v6
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v7
+        uses: actions/setup-python@v6
         with:
           python-version-file: "src/${{ matrix.package }}/.python-version"
 
@@ -73,10 +73,10 @@ jobs:
       - uses: actions/checkout@v6
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v7
+        uses: actions/setup-python@v6
         with:
           python-version-file: "src/${{ matrix.package }}/.python-version"
 
@@ -93,7 +93,7 @@ jobs:
         run: uv build
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v7
+        uses: actions/upload-artifact@v6
         with:
           name: dist-${{ matrix.package }}
           path: src/${{ matrix.package }}/dist/

.github/workflows/readme-pr-check.yml

@@ -1,10 +1,7 @@
 name: README PR Check
 
 on:
-  # pull_request_target, not pull_request: fork PRs get a read-only token under
-  # pull_request, so the label and comment calls fail with 403. This job only
-  # calls the API and never checks out PR code, so the write token is safe.
-  pull_request_target:
+  pull_request:
     types: [opened]
     paths:
       - 'README.md'
@@ -13,7 +10,7 @@ on:
 
 jobs:
   check-readme-only:
-    if: github.event_name == 'pull_request_target'
+    if: github.event_name == 'pull_request'
     runs-on: ubuntu-latest
     permissions:
       contents: read

.github/workflows/release.yml

@@ -25,7 +25,7 @@ jobs:
           echo "Using last release hash: ${HASH}"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v5
 
       - name: Create version name
         id: create-version
@@ -41,7 +41,7 @@ jobs:
           cat RELEASE_NOTES.md
 
       - name: Release notes
-        uses: actions/upload-artifact@v7
+        uses: actions/upload-artifact@v6
         with:
           name: release-notes
           path: RELEASE_NOTES.md
@@ -77,7 +77,7 @@ jobs:
           fetch-depth: 0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v5
 
       - name: Update packages
         run: |
@@ -121,10 +121,10 @@ jobs:
           ref: ${{ needs.create-metadata.outputs.version }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v5
 
       - name: Set up Python
-        uses: actions/setup-python@v7
+        uses: actions/setup-python@v6
         with:
           python-version-file: "src/${{ matrix.package }}/.python-version"
 
@@ -173,7 +173,7 @@ jobs:
         with:
           ref: ${{ needs.create-metadata.outputs.version }}
 
-      - uses: actions/setup-node@v7
+      - uses: actions/setup-node@v6
         with:
           node-version: 22
           cache: npm
@@ -228,7 +228,7 @@ jobs:
       - uses: actions/checkout@v6
 
       - name: Download release notes
-        uses: actions/download-artifact@v8
+        uses: actions/download-artifact@v7
         with:
           name: release-notes
 

.github/workflows/typescript.yml

@@ -34,7 +34,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: actions/setup-node@v7
+      - uses: actions/setup-node@v6
         with:
           node-version: 22
           cache: npm
@@ -57,7 +57,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: actions/setup-node@v7
+      - uses: actions/setup-node@v6
         with:
           node-version: 22
           cache: npm

README.md

@@ -39,7 +39,7 @@ These servers aim to demonstrate MCP features and the official SDKs.
 The following reference servers are now archived and can be found at [servers-archived](https://github.com/modelcontextprotocol/servers-archived).
 
 - **[AWS KB Retrieval](https://github.com/modelcontextprotocol/servers-archived/tree/main/src/aws-kb-retrieval-server)** - Retrieval from AWS Knowledge Base using Bedrock Agent Runtime.
-- **[Brave Search](https://github.com/modelcontextprotocol/servers-archived/tree/main/src/brave-search)** - Web and local search using Brave's Search API. Has been replaced by the [official server](https://github.com/brave/brave-search-mcp-server) ([`@brave/brave-search-mcp-server`](https://www.npmjs.com/package/@brave/brave-search-mcp-server)).
+- **[Brave Search](https://github.com/modelcontextprotocol/servers-archived/tree/main/src/brave-search)** - Web and local search using Brave's Search API.  Has been replaced by the [official server](https://github.com/brave/brave-search-mcp-server).
 - **[EverArt](https://github.com/modelcontextprotocol/servers-archived/tree/main/src/everart)** - AI image generation using various models.
 - **[GitHub](https://github.com/modelcontextprotocol/servers-archived/tree/main/src/github)** - Repository management, file operations, and GitHub API integration.
 - **[GitLab](https://github.com/modelcontextprotocol/servers-archived/tree/main/src/gitlab)** - GitLab API, enabling project management.

src/everything/README.md

@@ -113,7 +113,7 @@ npm run start:streamableHttp
 ### Install 
 ```shell
 npm install -g @modelcontextprotocol/server-everything@latest
-```
+````
 
 ### Run the default (stdio) server
 ```shell

src/everything/docs/startup.md

@@ -54,7 +54,7 @@
     - `prompts: {}`
     - `resources: { subscribe: true }`
   - **Server Instructions**
-    - Loaded from the docs folder (`instructions.md`).
+    - Loaded from the docs folder (`server-instructions.md`).
   - **Registrations**
     - Registers **tools** via `registerTools(server)`.
     - Registers **resources** via `registerResources(server)`.

src/everything/docs/structure.md

@@ -85,19 +85,9 @@ src/everything
 ### `docs/`
 
 - `architecture.md`
-  - Describes the server architecture, including transport layers, session initialization, and primitive registration.
-- `extension.md`
-  - Explains how to extend the server with new tools, prompts, resources, or transports.
-- `features.md`
-  - A comprehensive reference listing all implemented prompts, resources, tools, and protocol behaviors.
-- `how-it-works.md`
-  - Explains how SSE and Streamable HTTP transports are set up and how sessions are managed.
+  - This document.
 - `instructions.md`
   - Human‑readable instructions intended to be passed to the client/LLM as guidance on server use. Loaded by the server at startup and returned in the initialize exchange.
-- `startup.md`
-  - Describes the server startup sequence, environment checks, and initialization.
-- `structure.md`
-  - This document.
 
 ### `prompts/`
 

src/everything/package.json

@@ -30,7 +30,7 @@
     "test": "vitest run --coverage"
   },
   "dependencies": {
-    "@modelcontextprotocol/sdk": "^1.30.0",
+    "@modelcontextprotocol/sdk": "^1.29.0",
     "cors": "^2.8.5",
     "express": "^5.2.1",
     "jszip": "^3.10.1",
@@ -41,7 +41,7 @@
     "@types/express": "^5.0.6",
     "@vitest/coverage-v8": "^4.1.8",
     "prettier": "^2.8.8",
-    "shx": "^0.4.0",
+    "shx": "^0.3.4",
     "typescript": "^5.6.2",
     "vitest": "^4.1.8"
   }

src/everything/resources/subscriptions.ts

@@ -99,9 +99,10 @@ export const setSubscriptionHandlers = (server: McpServer) => {
 /**
  * Sends simulated resource update notifications to the subscribed client.
  *
- * Iterates the URIs in `subscriptions` and emits a
- * `notifications/resources/updated` notification for each URI the given
- * sessionId is subscribed to.
+ * This function iterates through all resource URIs stored in the subscriptions
+ * and checks if the specified session ID is subscribed to them. If so, it sends
+ * a notification through the provided server. If the session ID is no longer valid
+ * (disconnected), it removes the session ID from the list of subscribers.
  *
  * @param {McpServer} server - The server instance used to send notifications.
  * @param {string | undefined} sessionId - The session ID of the client to check for subscriptions.
@@ -121,6 +122,8 @@ const sendSimulatedResourceUpdates = async (
         method: "notifications/resources/updated",
         params: { uri },
       });
+    } else {
+      subscribers.delete(sessionId); // subscriber has disconnected
     }
   }
 };

src/everything/resources/templates.ts

@@ -127,26 +127,31 @@ export const blobResourceUri = (resourceId: number) =>
   new URL(`${blobUriBase}/${resourceId}`);
 
 /**
- * Parses the resource identifier from the provided variables and validates
- * that it is a positive integer.
+ * Parses the resource identifier from the provided URI and validates it
+ * against the given variables. Throws an error if the URI corresponds
+ * to an unknown resource or if the resource identifier is invalid.
  *
- * The SDK only routes URIs that match the registered template to the
- * resource handler, so by the time we get here the URI prefix is already
- * known to be one of `textUriBase` / `blobUriBase`. Only the resourceId
- * variable still needs validating.
- *
- * @param {URL} uri - The URI of the resource (used in the error message).
- * @param {Record<string, unknown>} variables - Context variables including resourceId.
- * @returns {number} The parsed and validated resource identifier as a positive integer.
- * @throws {Error} If the resourceId is not a finite positive integer.
+ * @param {URL} uri - The URI of the resource to be parsed.
+ * @param {Record<string, unknown>} variables - A record containing context-specific variables that include the resourceId.
+ * @returns {number} The parsed and validated resource identifier as an integer.
+ * @throws {Error} Throws an error if the URI matches unsupported base URIs or if the resourceId is invalid.
  */
 const parseResourceId = (uri: URL, variables: Record<string, unknown>) => {
-  const idxStr = String((variables as any).resourceId ?? "");
-  const idx = Number(idxStr);
-  if (Number.isFinite(idx) && Number.isInteger(idx) && idx > 0) {
-    return idx;
+  const uriError = `Unknown resource: ${uri.toString()}`;
+  if (
+    uri.toString().startsWith(textUriBase) &&
+    uri.toString().startsWith(blobUriBase)
+  ) {
+    throw new Error(uriError);
+  } else {
+    const idxStr = String((variables as any).resourceId ?? "");
+    const idx = Number(idxStr);
+    if (Number.isFinite(idx) && Number.isInteger(idx) && idx > 0) {
+      return idx;
+    } else {
+      throw new Error(uriError);
+    }
   }
-  throw new Error(`Unknown resource: ${uri.toString()}`);
 };
 
 /**

src/fetch/Dockerfile

@@ -11,8 +11,9 @@ ENV UV_COMPILE_BYTECODE=1
 ENV UV_LINK_MODE=copy
 
 # Install the project's dependencies using the lockfile and settings
-COPY uv.lock pyproject.toml ./
 RUN --mount=type=cache,target=/root/.cache/uv \
+    --mount=type=bind,source=uv.lock,target=uv.lock \
+    --mount=type=bind,source=pyproject.toml,target=pyproject.toml \
     uv sync --locked --no-install-project --no-dev --no-editable
 
 # Then, add the rest of the project source code and install it
@@ -26,10 +27,6 @@ FROM python:3.12-slim-bookworm
 WORKDIR /app
  
 COPY --from=uv /root/.local /root/.local
-
-RUN if ! id -u app >/dev/null 2>&1; then \
-      useradd -rUM -s /usr/sbin/nologin app; \
-    fi
 COPY --from=uv --chown=app:app /app/.venv /app/.venv
 
 # Place executables in the environment at the front of the path

src/fetch/README.md

@@ -6,8 +6,6 @@ A Model Context Protocol server that provides web content fetching capabilities.
 
 Source: https://github.com/modelcontextprotocol/servers/tree/main/src/fetch
 
-Requires MCP Python SDK 1.x (`mcp>=1.29.0,<2`). SDK 2.0 renamed APIs this server uses. The port to v2 is in progress.
-
 > [!CAUTION]
 > This server can access local/internal IP addresses and may represent a security risk. Exercise caution when using this MCP server to ensure this does not expose any sensitive data.
 

src/fetch/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mcp-server-fetch"
-version = "0.6.3"
+version = "2026.7.10"
 description = "A Model Context Protocol server providing tools to fetch and convert web content for usage by LLMs"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -18,7 +18,7 @@ classifiers = [
 dependencies = [
     "httpx>=0.27",
     "markdownify>=0.13.1",
-    "mcp>=1.29.0,<2",
+    "mcp>=1.1.3",
     "protego>=0.3.1",
     "pydantic>=2.0.0",
     "readabilipy>=0.2.0",

src/fetch/uv.lock

@@ -1,12 +1,6 @@
 version = 1
 revision = 3
 requires-python = ">=3.10"
-resolution-markers = [
-    "python_full_version >= '3.14' and sys_platform == 'win32'",
-    "python_full_version >= '3.14' and sys_platform != 'win32'",
-    "python_full_version < '3.14' and sys_platform == 'win32'",
-    "python_full_version < '3.14' and sys_platform != 'win32'",
-]
 
 [[package]]
 name = "annotated-types"
@@ -539,7 +533,7 @@ wheels = [
 
 [[package]]
 name = "mcp"
-version = "1.29.0"
+version = "1.23.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "anyio" },
@@ -557,14 +551,14 @@ dependencies = [
     { name = "typing-inspection" },
     { name = "uvicorn", marker = "sys_platform != 'emscripten'" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/30/d3/f9acc21dfc886e4f78e2add1a47db46ce16884346afde53f8a064c02c891/mcp-1.29.0.tar.gz", hash = "sha256:52d01f334de1868cc3bb2d6604931126a67631f99a6c5d3b82ba47290315ec36", size = 643148, upload-time = "2026-07-28T13:41:41.939Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/25/1a/9c8a5362e3448d585081d6c7aa95898a64e0ac59d3e26169ae6c3ca5feaf/mcp-1.23.0.tar.gz", hash = "sha256:84e0c29316d0a8cf0affd196fd000487ac512aa3f771b63b2ea864e22961772b", size = 596506, upload-time = "2025-12-02T13:40:02.558Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/01/c8/248b201f6d753d69fd5d6506011abbb35a946d9142b2ae311a948fd0be3d/mcp-1.29.0-py3-none-any.whl", hash = "sha256:f5a075bb611f23d6f4d080c6a1699fa62772eebc562ba9e66b306ddde1c755f7", size = 223436, upload-time = "2026-07-28T13:41:40.337Z" },
+    { url = "https://files.pythonhosted.org/packages/7b/b2/28739ce409f98159c0121eab56e69ad71546c4f34ac8b42e58c03f57dccc/mcp-1.23.0-py3-none-any.whl", hash = "sha256:5a645cf111ed329f4619f2629a3f15d9aabd7adc2ea09d600d31467b51ecb64f", size = 231427, upload-time = "2025-12-02T13:40:00.738Z" },
 ]
 
 [[package]]
 name = "mcp-server-fetch"
-version = "0.6.3"
+version = "2026.7.10"
 source = { editable = "." }
 dependencies = [
     { name = "httpx" },
@@ -588,7 +582,7 @@ dev = [
 requires-dist = [
     { name = "httpx", specifier = ">=0.27" },
     { name = "markdownify", specifier = ">=0.13.1" },
-    { name = "mcp", specifier = ">=1.29.0,<2" },
+    { name = "mcp", specifier = ">=1.1.3" },
     { name = "protego", specifier = ">=0.3.1" },
     { name = "pydantic", specifier = ">=2.0.0" },
     { name = "readabilipy", specifier = ">=0.2.0" },
@@ -1185,11 +1179,11 @@ wheels = [
 
 [[package]]
 name = "soupsieve"
-version = "2.8.4"
+version = "2.6"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/47/2c/0a5f6f8ee0d5589e48c7640213ed5175d52cf540a06725b628cc1a45d6ce/soupsieve-2.8.4.tar.gz", hash = "sha256:e121fd02e975c695e4e9e8774a5ee35d74714b59307868dcc5319ad2d9e3328e", size = 121110, upload-time = "2026-05-24T13:55:57.154Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/d7/ce/fbaeed4f9fb8b2daa961f90591662df6a86c1abf25c548329a86920aedfb/soupsieve-2.6.tar.gz", hash = "sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb", size = 101569, upload-time = "2024-08-13T13:39:12.166Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/5e/f5/0c41cb68dcae6b7de4fac4188a3a9589e21fb31df21ea3a2e888db95e6c9/soupsieve-2.8.4-py3-none-any.whl", hash = "sha256:e7e6b0769c8f51ed59acab6e994b00621096cfb1c640a7509295987388fbaf65", size = 37304, upload-time = "2026-05-24T13:55:55.406Z" },
+    { url = "https://files.pythonhosted.org/packages/d1/c2/fe97d779f3ef3b15f05c94a2f1e3d21732574ed441687474db9d342a7315/soupsieve-2.6-py3-none-any.whl", hash = "sha256:e72c4ff06e4fb6e4b5a9f0f55fe6e81514581fca1515028625d0f299c602ccc9", size = 36186, upload-time = "2024-08-13T13:39:10.986Z" },
 ]
 
 [[package]]

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

@@ -1,57 +0,0 @@
-import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import * as fs from 'fs/promises';
-import * as path from 'path';
-import * as os from 'os';
-import { Client } from '@modelcontextprotocol/sdk/client/index.js';
-import { StdioClientTransport } from '@modelcontextprotocol/sdk/client/stdio.js';
-
-describe('directory_tree MCP SDK regression', () => {
-  let client: Client;
-  let transport: StdioClientTransport;
-  let testDir: string;
-
-  beforeEach(async () => {
-    const tmp = await fs.mkdtemp(path.join(os.tmpdir(), 'mcp-fs-tree-'));
-    testDir = await fs.realpath(tmp);
-
-    await fs.writeFile(path.join(testDir, 'root.txt'), 'root');
-    await fs.mkdir(path.join(testDir, 'nested'));
-    await fs.writeFile(path.join(testDir, 'nested', 'child.txt'), 'child');
-
-    const serverPath = path.resolve(__dirname, '../dist/index.js');
-    transport = new StdioClientTransport({
-      command: 'node',
-      args: [serverPath, testDir],
-    });
-
-    client = new Client(
-      { name: 'directory-tree-regression-test', version: '1.0.0' },
-      { capabilities: {} },
-    );
-
-    await client.connect(transport);
-  });
-
-  afterEach(async () => {
-    await client?.close();
-    await fs.rm(testDir, { recursive: true, force: true });
-  });
-
-  it('returns structuredContent.content as a string (not an array) when called via MCP SDK', async () => {
-    const result = await client.callTool({
-      name: 'directory_tree',
-      arguments: { path: testDir },
-    });
-
-    // Regression test for issues where structuredContent was returned as an array,
-    // which causes MCP SDK validation to throw -32602 (invalid structured content).
-    const structured = result.structuredContent as { content: unknown };
-    expect(structured).toBeDefined();
-    expect(typeof structured.content).toBe('string');
-    expect(Array.isArray(structured.content)).toBe(false);
-
-    const parsed = JSON.parse(structured.content as string);
-    expect(Array.isArray(parsed)).toBe(true);
-    expect(parsed.length).toBeGreaterThan(0);
-  });
-});

src/filesystem/__tests__/lib.test.ts

@@ -14,7 +14,6 @@ import {
   getFileStats,
   readFileContent,
   writeFileContent,
-  moveFile,
   // Search & filtering functions
   searchFilesWithValidation,
   // File editing functions
@@ -27,23 +26,6 @@ import {
 vi.mock('fs/promises');
 const mockFs = fs as any;
 
-function createMockFileHandle(content: Buffer) {
-  return {
-    read: vi.fn(
-      async (buffer: Buffer, offset: number, length: number, position: number) => {
-        const bytesRead = content.copy(
-          buffer,
-          offset,
-          position,
-          Math.min(position + length, content.length),
-        );
-        return { bytesRead, buffer };
-      },
-    ),
-    close: vi.fn().mockResolvedValue(undefined),
-  };
-}
-
 describe('Lib Functions', () => {
   beforeEach(() => {
     vi.clearAllMocks();
@@ -83,10 +65,8 @@ describe('Lib Functions', () => {
       });
 
       it('handles negative numbers', () => {
-        // Negative numbers should return '0 B' as file sizes cannot be negative
-        expect(formatSize(-1)).toBe('0 B');
-        expect(formatSize(-1024)).toBe('0 B');
-        expect(formatSize(-1000000)).toBe('0 B');
+        // Negative numbers will result in NaN for the log calculation
+        expect(formatSize(-1024)).toContain('NaN');
         expect(formatSize(-0)).toBe('0 B');
       });
 
@@ -173,13 +153,6 @@ describe('Lib Functions', () => {
 
   describe('Security & Validation Functions', () => {
     describe('validatePath', () => {
-      it('rejects Windows drive paths on POSIX hosts', async () => {
-        if (process.platform === 'win32') return;
-
-        await expect(validatePath('C:\\Users\\me\\notes\\file.md'))
-          .rejects.toThrow('Windows-style path received on a POSIX host');
-      });
-
       // Use Windows-compatible paths for testing
       const allowedDirs = process.platform === 'win32' ? ['C:\\Users\\test', 'C:\\temp'] : ['/home/user', '/tmp'];
 
@@ -215,34 +188,19 @@ describe('Lib Functions', () => {
         expect(result).toBe(path.resolve(newFilePath));
       });
 
-      it('walks past multiple missing ancestors to an existing allowed directory', async () => {
-        // e.g. create_directory('/home/user/nonexistent/nested/newfile.txt') when
-        // neither 'nonexistent' nor 'nonexistent/nested' exist yet, but '/home/user'
-        // (an allowed directory) does. Regression test for #4629.
-        const newFilePath = process.platform === 'win32' ? 'C:\\Users\\test\\nonexistent\\nested\\newfile.txt' : '/home/user/nonexistent/nested/newfile.txt';
-
-        const enoentError = new Error('ENOENT') as NodeJS.ErrnoException;
-        enoentError.code = 'ENOENT';
-
-        // The path itself is missing. The resolver then realpaths the allowed
-        // directory ('/home/user'), which falls through to the beforeEach base
-        // implementation and echoes the path back as-is. readdir is mocked to
-        // undefined, so every component below it counts as missing.
-        mockFs.realpath.mockRejectedValueOnce(enoentError);
-
-        const result = await validatePath(newFilePath);
-        expect(result).toBe(path.resolve(newFilePath));
-      });
-
-      it('rejects when no ancestor directory exists at all', async () => {
+      it('rejects when parent directory does not exist', async () => {
         const newFilePath = process.platform === 'win32' ? 'C:\\Users\\test\\nonexistent\\newfile.txt' : '/home/user/nonexistent/newfile.txt';
-
-        const enoentError = new Error('ENOENT') as NodeJS.ErrnoException;
-        enoentError.code = 'ENOENT';
-
-        // Every ancestor, all the way up to the filesystem root, is missing.
-        mockFs.realpath.mockRejectedValue(enoentError);
-
+        
+        // Create errors with the ENOENT code
+        const enoentError1 = new Error('ENOENT') as NodeJS.ErrnoException;
+        enoentError1.code = 'ENOENT';
+        const enoentError2 = new Error('ENOENT') as NodeJS.ErrnoException;
+        enoentError2.code = 'ENOENT';
+        
+        mockFs.realpath
+          .mockRejectedValueOnce(enoentError1)
+          .mockRejectedValueOnce(enoentError2);
+        
         await expect(validatePath(newFilePath))
           .rejects.toThrow('Parent directory does not exist');
       });
@@ -350,56 +308,6 @@ describe('Lib Functions', () => {
         
         expect(mockFs.writeFile).toHaveBeenCalledWith('/test/file.txt', 'new content', { encoding: "utf-8", flag: 'wx' });
       });
-
-      it('preserves file permissions when overwriting existing file', async () => {
-        // First writeFile call with 'wx' flag fails because file exists
-        mockFs.writeFile.mockRejectedValueOnce(Object.assign(new Error('EEXIST'), { code: 'EEXIST' }));
-        // stat returns executable permissions
-        mockFs.stat.mockResolvedValueOnce({ mode: 0o100755 });
-        // Second writeFile (to temp) succeeds
-        mockFs.writeFile.mockResolvedValueOnce(undefined);
-        mockFs.rename.mockResolvedValueOnce(undefined);
-        mockFs.chmod.mockResolvedValueOnce(undefined);
-
-        await writeFileContent('/test/script.sh', 'new content');
-
-        expect(mockFs.stat).toHaveBeenCalledWith('/test/script.sh');
-        expect(mockFs.chmod).toHaveBeenCalledWith('/test/script.sh', 0o755);
-      });
-
-      it('does not fail the write when chmod fails', async () => {
-        mockFs.writeFile.mockRejectedValueOnce(Object.assign(new Error('EEXIST'), { code: 'EEXIST' }));
-        mockFs.stat.mockResolvedValueOnce({ mode: 0o100755 });
-        mockFs.writeFile.mockResolvedValueOnce(undefined);
-        mockFs.rename.mockResolvedValueOnce(undefined);
-        mockFs.chmod.mockRejectedValueOnce(Object.assign(new Error('EPERM'), { code: 'EPERM' }));
-
-        await expect(writeFileContent('/test/script.sh', 'new content')).resolves.toBeUndefined();
-        expect(mockFs.unlink).not.toHaveBeenCalled();
-      });
-    });
-
-    describe('moveFile', () => {
-      it('moves the file when the destination does not exist', async () => {
-        const enoent = Object.assign(new Error('not found'), { code: 'ENOENT' });
-        mockFs.lstat.mockRejectedValueOnce(enoent);
-        mockFs.rename.mockResolvedValueOnce(undefined);
-
-        await moveFile('/test/source.txt', '/test/dest.txt');
-
-        expect(mockFs.rename).toHaveBeenCalledWith('/test/source.txt', '/test/dest.txt');
-      });
-
-      it('fails without overwriting when the destination already exists', async () => {
-        // lstat resolving means the destination is occupied.
-        mockFs.lstat.mockResolvedValueOnce({} as any);
-
-        await expect(moveFile('/test/source.txt', '/test/dest.txt')).rejects.toThrow(
-          'Destination already exists'
-        );
-
-        expect(mockFs.rename).not.toHaveBeenCalled();
-      });
     });
 
   });
@@ -508,8 +416,6 @@ describe('Lib Functions', () => {
       beforeEach(() => {
         mockFs.readFile.mockResolvedValue('line1\nline2\nline3\n');
         mockFs.writeFile.mockResolvedValue(undefined);
-        mockFs.stat.mockResolvedValue({ mode: 0o100644 });
-        mockFs.chmod.mockResolvedValue(undefined);
       });
 
       it('applies simple text replacement', async () => {
@@ -604,30 +510,6 @@ describe('Lib Functions', () => {
         );
       });
 
-      it('preserves file permissions after applying edits', async () => {
-        mockFs.stat.mockResolvedValue({ mode: 0o100755 });
-        const edits = [
-          { oldText: 'line2', newText: 'modified line2' }
-        ];
-        
-        mockFs.rename.mockResolvedValueOnce(undefined);
-        
-        await applyFileEdits('/test/script.sh', edits, false);
-        
-        expect(mockFs.stat).toHaveBeenCalledWith('/test/script.sh');
-        expect(mockFs.chmod).toHaveBeenCalledWith('/test/script.sh', 0o755);
-      });
-
-      it('does not restore permissions in dry run mode', async () => {
-        const edits = [
-          { oldText: 'line2', newText: 'modified line2' }
-        ];
-        
-        await applyFileEdits('/test/file.txt', edits, true);
-        
-        expect(mockFs.chmod).not.toHaveBeenCalled();
-      });
-
       it('throws error for non-matching edits', async () => {
         const edits = [
           { oldText: 'nonexistent line', newText: 'replacement' }
@@ -761,23 +643,6 @@ describe('Lib Functions', () => {
         expect(mockFileHandle.close).toHaveBeenCalled();
       });
 
-      it('preserves UTF-8 characters split across chunk boundaries', async () => {
-        const content = Buffer.concat([
-          Buffer.from('discard\n'),
-          Buffer.from('界'),
-          Buffer.alloc(1017, 'a'),
-          Buffer.from('\nlast'),
-        ]);
-        const mockFileHandle = createMockFileHandle(content);
-
-        mockFs.stat.mockResolvedValue({ size: content.length } as any);
-        mockFs.open.mockResolvedValue(mockFileHandle);
-
-        const result = await tailFile('/test/file.txt', 2);
-
-        expect(result).toBe(`界${'a'.repeat(1017)}\nlast`);
-      });
-
       it('handles read errors gracefully', async () => {
         mockFs.stat.mockResolvedValue({ size: 100 } as any);
         
@@ -834,20 +699,6 @@ describe('Lib Functions', () => {
         expect(mockFileHandle.close).toHaveBeenCalled();
       });
 
-      it('preserves UTF-8 characters split across chunk boundaries', async () => {
-        const content = Buffer.concat([
-          Buffer.alloc(1023, 'a'),
-          Buffer.from('界\nsecond'),
-        ]);
-        const mockFileHandle = createMockFileHandle(content);
-
-        mockFs.open.mockResolvedValue(mockFileHandle);
-
-        const result = await headFile('/test/file.txt', 1);
-
-        expect(result).toBe(`${'a'.repeat(1023)}界`);
-      });
-
       it('handles files with leftover content', async () => {
         const mockFileHandle = {
           read: vi.fn(),

src/filesystem/__tests__/nested-parents.test.ts

@@ -1,35 +0,0 @@
-import fs from 'fs/promises';
-import os from 'os';
-import path from 'path';
-import { afterEach, beforeEach, describe, expect, it } from 'vitest';
-import { setAllowedDirectories, validatePath } from '../lib.js';
-
-// Regression coverage for #4629: validatePath must accept a path whose
-// ancestors are missing several levels deep, so create_directory can mkdir -p.
-describe('validatePath with multiple missing ancestors', () => {
-  let allowedDir: string;
-  let outsideDir: string;
-
-  beforeEach(async () => {
-    allowedDir = await fs.realpath(await fs.mkdtemp(path.join(os.tmpdir(), 'mcp-nested-allowed-')));
-    outsideDir = await fs.realpath(await fs.mkdtemp(path.join(os.tmpdir(), 'mcp-nested-outside-')));
-    setAllowedDirectories([allowedDir]);
-  });
-
-  afterEach(async () => {
-    setAllowedDirectories([]);
-    await fs.rm(allowedDir, { recursive: true, force: true });
-    await fs.rm(outsideDir, { recursive: true, force: true });
-  });
-
-  it('returns the full path when several ancestors do not exist', async () => {
-    const requested = path.join(allowedDir, 'a', 'b', 'c');
-    await expect(validatePath(requested)).resolves.toBe(requested);
-  });
-
-  it('rejects when the nearest existing ancestor is a symlink out of the allowed tree', async () => {
-    await fs.symlink(outsideDir, path.join(allowedDir, 'link'), 'junction');
-    await expect(validatePath(path.join(allowedDir, 'link', 'a', 'b')))
-      .rejects.toThrow('Access denied');
-  });
-});