fix(memory): serialize graph mutations to prevent concurrent write race (#4555)

createEntities, createRelations, addObservations, deleteEntities,
deleteObservations, and deleteRelations each independently did
load -> mutate -> save with no synchronization. Concurrent tool
calls (e.g. multiple mutations dispatched from one LLM turn) could
race: both read the same starting state, both write back their own
copy, and whichever write landed last silently discarded the other's
changes. Interleaved writes could also corrupt the file outright.

Adds an in-process async mutex (KnowledgeGraphManager.withLock) that
serializes all six mutation methods through a single queue. Read-only
methods (readGraph, searchNodes, openNodes) are unaffected.

Verified: reverting the fix and re-running the new concurrency tests
reproduces the bug exactly (lost entities, lost relations, malformed
JSONL lines). With the fix, all 39 tests pass.

Fixes #1819

Co-authored-by: olaservo <olahungerford@gmail.com>

.github/dependabot.yml

@@ -0,0 +1,6 @@
+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@v3
+        uses: astral-sh/setup-uv@v7
 
       - name: Set up Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         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@v3
+        uses: astral-sh/setup-uv@v7
 
       - name: Set up Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version-file: "src/${{ matrix.package }}/.python-version"
 
@@ -93,7 +93,7 @@ jobs:
         run: uv build
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: dist-${{ matrix.package }}
           path: src/${{ matrix.package }}/dist/

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

@@ -1,7 +1,10 @@
 name: README PR Check
 
 on:
-  pull_request:
+  # 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:
     types: [opened]
     paths:
       - 'README.md'
@@ -10,7 +13,7 @@ on:
 
 jobs:
   check-readme-only:
-    if: github.event_name == 'pull_request'
+    if: github.event_name == 'pull_request_target'
     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@v5
+        uses: astral-sh/setup-uv@v7
 
       - name: Create version name
         id: create-version
@@ -41,7 +41,7 @@ jobs:
           cat RELEASE_NOTES.md
 
       - name: Release notes
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: release-notes
           path: RELEASE_NOTES.md
@@ -77,7 +77,7 @@ jobs:
           fetch-depth: 0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
 
       - name: Update packages
         run: |
@@ -121,10 +121,10 @@ jobs:
           ref: ${{ needs.create-metadata.outputs.version }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
 
       - name: Set up Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         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@v6
+      - uses: actions/setup-node@v7
         with:
           node-version: 22
           cache: npm
@@ -228,7 +228,7 @@ jobs:
       - uses: actions/checkout@v6
 
       - name: Download release notes
-        uses: actions/download-artifact@v7
+        uses: actions/download-artifact@v8
         with:
           name: release-notes
 

.github/workflows/typescript.yml

@@ -34,7 +34,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: actions/setup-node@v6
+      - uses: actions/setup-node@v7
         with:
           node-version: 22
           cache: npm
@@ -57,7 +57,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: actions/setup-node@v6
+      - uses: actions/setup-node@v7
         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 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)).
 - **[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 (`server-instructions.md`).
+    - Loaded from the docs folder (`instructions.md`).
   - **Registrations**
     - Registers **tools** via `registerTools(server)`.
     - Registers **resources** via `registerResources(server)`.

src/everything/docs/structure.md

@@ -85,9 +85,19 @@ src/everything
 ### `docs/`
 
 - `architecture.md`
-  - This document.
+  - 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.
 - `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": "^1.29.0",
+    "@modelcontextprotocol/sdk": "^1.30.0",
     "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": "^0.3.4",
+    "shx": "^0.4.0",
     "typescript": "^5.6.2",
     "vitest": "^4.1.8"
   }

src/everything/resources/subscriptions.ts

@@ -99,10 +99,9 @@ export const setSubscriptionHandlers = (server: McpServer) => {
 /**
  * Sends simulated resource update notifications to the subscribed client.
  *
- * 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.
+ * Iterates the URIs in `subscriptions` and emits a
+ * `notifications/resources/updated` notification for each URI the given
+ * sessionId is subscribed to.
  *
  * @param {McpServer} server - The server instance used to send notifications.
  * @param {string | undefined} sessionId - The session ID of the client to check for subscriptions.
@@ -122,8 +121,6 @@ const sendSimulatedResourceUpdates = async (
         method: "notifications/resources/updated",
         params: { uri },
       });
-    } else {
-      subscribers.delete(sessionId); // subscriber has disconnected
     }
   }
 };

src/everything/resources/templates.ts

@@ -127,31 +127,26 @@ export const blobResourceUri = (resourceId: number) =>
   new URL(`${blobUriBase}/${resourceId}`);
 
 /**
- * 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.
+ * Parses the resource identifier from the provided variables and validates
+ * that it is a 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.
+ * 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.
  */
 const parseResourceId = (uri: URL, variables: Record<string, unknown>) => {
-  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);
-    }
+  const idxStr = String((variables as any).resourceId ?? "");
+  const idx = Number(idxStr);
+  if (Number.isFinite(idx) && Number.isInteger(idx) && idx > 0) {
+    return idx;
   }
+  throw new Error(`Unknown resource: ${uri.toString()}`);
 };
 
 /**

src/fetch/Dockerfile

@@ -11,9 +11,8 @@ 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
@@ -27,6 +26,10 @@ 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

@@ -6,6 +6,8 @@ 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

@@ -18,7 +18,7 @@ classifiers = [
 dependencies = [
     "httpx>=0.27",
     "markdownify>=0.13.1",
-    "mcp>=1.1.3",
+    "mcp>=1.29.0,<2",
     "protego>=0.3.1",
     "pydantic>=2.0.0",
     "readabilipy>=0.2.0",

src/fetch/uv.lock

@@ -1,6 +1,12 @@
 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"
@@ -533,7 +539,7 @@ wheels = [
 
 [[package]]
 name = "mcp"
-version = "1.23.0"
+version = "1.29.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "anyio" },
@@ -551,9 +557,9 @@ dependencies = [
     { name = "typing-inspection" },
     { name = "uvicorn", marker = "sys_platform != 'emscripten'" },
 ]
-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" }
+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" }
 wheels = [
-    { 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" },
+    { 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" },
 ]
 
 [[package]]
@@ -582,7 +588,7 @@ dev = [
 requires-dist = [
     { name = "httpx", specifier = ">=0.27" },
     { name = "markdownify", specifier = ">=0.13.1" },
-    { name = "mcp", specifier = ">=1.1.3" },
+    { name = "mcp", specifier = ">=1.29.0,<2" },
     { name = "protego", specifier = ">=0.3.1" },
     { name = "pydantic", specifier = ">=2.0.0" },
     { name = "readabilipy", specifier = ">=0.2.0" },
@@ -1179,11 +1185,11 @@ wheels = [
 
 [[package]]
 name = "soupsieve"
-version = "2.6"
+version = "2.8.4"
 source = { registry = "https://pypi.org/simple" }
-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" }
+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" }
 wheels = [
-    { 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" },
+    { 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" },
 ]
 
 [[package]]

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

@@ -0,0 +1,57 @@
+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

@@ -14,6 +14,7 @@ import {
   getFileStats,
   readFileContent,
   writeFileContent,
+  moveFile,
   // Search & filtering functions
   searchFilesWithValidation,
   // File editing functions
@@ -26,6 +27,23 @@ 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();
@@ -65,8 +83,10 @@ describe('Lib Functions', () => {
       });
 
       it('handles negative numbers', () => {
-        // Negative numbers will result in NaN for the log calculation
-        expect(formatSize(-1024)).toContain('NaN');
+        // 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');
         expect(formatSize(-0)).toBe('0 B');
       });
 
@@ -153,6 +173,13 @@ 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'];
 
@@ -188,19 +215,34 @@ describe('Lib Functions', () => {
         expect(result).toBe(path.resolve(newFilePath));
       });
 
-      it('rejects when parent directory does not exist', async () => {
+      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 () => {
         const newFilePath = process.platform === 'win32' ? 'C:\\Users\\test\\nonexistent\\newfile.txt' : '/home/user/nonexistent/newfile.txt';
-        
-        // 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);
-        
+
+        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);
+
         await expect(validatePath(newFilePath))
           .rejects.toThrow('Parent directory does not exist');
       });
@@ -308,6 +350,56 @@ 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();
+      });
     });
 
   });
@@ -416,6 +508,8 @@ 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 () => {
@@ -510,6 +604,30 @@ 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' }
@@ -643,6 +761,23 @@ 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);
         
@@ -699,6 +834,20 @@ 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

@@ -0,0 +1,35 @@
+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');
+  });
+});