Automatic update of packages

.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

package-lock.json

@@ -3866,8 +3866,7 @@
         "@modelcontextprotocol/sdk": "^1.30.0",
         "diff": "^8.0.3",
         "glob": "^13.0.6",
-        "minimatch": "^10.0.1",
-        "zod": "^4.0.0"
+        "minimatch": "^10.0.1"
       },
       "bin": {
         "mcp-server-filesystem": "dist/index.js"
@@ -3887,8 +3886,7 @@
       "version": "0.6.3",
       "license": "SEE LICENSE IN LICENSE",
       "dependencies": {
-        "@modelcontextprotocol/sdk": "^1.30.0",
-        "zod": "^4.0.0"
+        "@modelcontextprotocol/sdk": "^1.30.0"
       },
       "bin": {
         "mcp-server-memory": "dist/index.js"
@@ -3908,8 +3906,7 @@
       "dependencies": {
         "@modelcontextprotocol/sdk": "^1.30.0",
         "chalk": "^5.3.0",
-        "yargs": "^17.7.2",
-        "zod": "^4.0.0"
+        "yargs": "^17.7.2"
       },
       "bin": {
         "mcp-server-sequential-thinking": "dist/index.js"

src/everything/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@modelcontextprotocol/server-everything",
-  "version": "2.0.0",
+  "version": "2026.8.31",
   "description": "MCP server that exercises all the features of the MCP protocol",
   "license": "SEE LICENSE IN LICENSE",
   "mcpName": "io.github.modelcontextprotocol/server-everything",
@@ -45,4 +45,4 @@
     "typescript": "^5.6.2",
     "vitest": "^4.1.8"
   }
-}
+}

src/filesystem/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@modelcontextprotocol/server-filesystem",
-  "version": "0.6.3",
+  "version": "2026.8.31",
   "description": "MCP server for filesystem access",
   "license": "SEE LICENSE IN LICENSE",
   "mcpName": "io.github.modelcontextprotocol/server-filesystem",
@@ -28,8 +28,7 @@
     "@modelcontextprotocol/sdk": "^1.30.0",
     "diff": "^8.0.3",
     "glob": "^13.0.6",
-    "minimatch": "^10.0.1",
-    "zod": "^4.0.0"
+    "minimatch": "^10.0.1"
   },
   "devDependencies": {
     "@types/diff": "^5.0.9",
@@ -40,4 +39,4 @@
     "typescript": "^5.8.2",
     "vitest": "^4.1.8"
   }
-}
+}

src/git/src/mcp_server_git/server.py

@@ -1,6 +1,6 @@
 import logging
 from pathlib import Path
-from typing import Any, Optional, Sequence
+from typing import Sequence, Optional
 from mcp.server import Server
 from mcp.server.session import ServerSession
 from mcp.server.stdio import stdio_server
@@ -157,28 +157,45 @@ def git_reset(repo: git.Repo) -> str:
     return "All staged changes reset"
 
 def git_log(repo: git.Repo, max_count: int = 10, start_timestamp: Optional[str] = None, end_timestamp: Optional[str] = None) -> list[str]:
-    # Defense in depth: reject timestamps starting with '-' to prevent flag injection
-    if start_timestamp and start_timestamp.startswith("-"):
-        raise ValueError(f"Invalid start_timestamp: '{start_timestamp}' - cannot start with '-'")
-    if end_timestamp and end_timestamp.startswith("-"):
-        raise ValueError(f"Invalid end_timestamp: '{end_timestamp}' - cannot start with '-'")
+    if start_timestamp or end_timestamp:
+        # Defense in depth: reject timestamps starting with '-' to prevent flag injection
+        if start_timestamp and start_timestamp.startswith("-"):
+            raise ValueError(f"Invalid start_timestamp: '{start_timestamp}' - cannot start with '-'")
+        if end_timestamp and end_timestamp.startswith("-"):
+            raise ValueError(f"Invalid end_timestamp: '{end_timestamp}' - cannot start with '-'")
+        # 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'])
 
-    kwargs: dict[str, Any] = {"max_count": max_count}
-    if start_timestamp:
-        kwargs["since"] = start_timestamp
-    if end_timestamp:
-        kwargs["until"] = end_timestamp
+        log_output = repo.git.log(*args).split('\n')
 
-    commits = list(repo.iter_commits(**kwargs))
-    log = []
-    for commit in commits:
-        log.append(
-            f"Commit: {commit.hexsha}\n"
-            f"Author: {commit.author}\n"
-            f"Date: {commit.authored_datetime}\n"
-            f"Message: {commit.message}\n"
-        )
-    return log
+        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:
     # Defense in depth: reject names starting with '-' to prevent flag injection
@@ -582,4 +599,4 @@ async def serve(repository: Path | None) -> None:
 
     options = server.create_initialization_options()
     async with stdio_server() as (read_stream, write_stream):
-        await server.run(read_stream, write_stream, options)
+        await server.run(read_stream, write_stream, options, raise_exceptions=True)

src/git/tests/test_server.py

@@ -16,10 +16,8 @@ from mcp_server_git.server import (
     git_create_branch,
     git_show,
     validate_repo_path,
-    serve,
 )
 import shutil
-import unittest.mock as mock
 
 @pytest.fixture
 def test_repository(tmp_path: Path):
@@ -510,81 +508,3 @@ def test_git_branch_rejects_contains_flag_injection(test_repository):
 
     with pytest.raises(BadName):
         git_branch(test_repository, "local", not_contains="--exec=evil")
-
-
-def test_git_log_formatting_no_repr(test_repository):
-    """Test that git_log does not use !r formatting (no Python object repr or quotes)."""
-    file_path = Path(test_repository.working_dir) / "multiline.txt"
-    file_path.write_text("multiline test")
-    test_repository.index.add(["multiline.txt"])
-    test_repository.index.commit("Subject line\n\nDetailed body line 1\nDetailed body line 2")
-
-    result = git_log(test_repository, max_count=1)
-    entry = result[0]
-
-    # Verify no python repr quotes around commit hash or message
-    assert "Commit: '" not in entry
-    assert 'Commit: "' not in entry
-    assert "<git.Actor" not in entry
-    assert "Message: '" not in entry
-    assert 'Message: "' not in entry
-
-    # Verify full message with body is included
-    assert "Subject line\n\nDetailed body line 1\nDetailed body line 2" in entry
-
-
-def test_git_log_filtered_unfiltered_parity(test_repository):
-    """Test that filtered and unfiltered git_log produce identical schema and preserve commit body."""
-    file_path = Path(test_repository.working_dir) / "parity_test.txt"
-    file_path.write_text("parity test")
-    test_repository.index.add(["parity_test.txt"])
-    test_repository.index.commit("Parity subject\n\nParity body line 1\nParity body line 2")
-
-    unfiltered = git_log(test_repository, max_count=1)
-    filtered_since = git_log(test_repository, max_count=1, start_timestamp="yesterday")
-    filtered_until = git_log(test_repository, max_count=1, end_timestamp="2099-01-01")
-
-    # Output schemas and contents must be identical
-    assert unfiltered == filtered_since
-    assert unfiltered == filtered_until
-
-    # Multi-line commit message preserved in filtered results
-    assert "Parity subject\n\nParity body line 1\nParity body line 2" in filtered_since[0]
-
-
-def test_git_log_date_filtering(test_repository):
-    """Test date filtering logic in git_log."""
-    # Future start_timestamp should return no commits
-    future_result = git_log(test_repository, start_timestamp="2099-01-01")
-    assert future_result == []
-
-    # Past end_timestamp should return no commits
-    past_result = git_log(test_repository, end_timestamp="2000-01-01")
-    assert past_result == []
-
-    # Valid range with max_count
-    valid_result = git_log(test_repository, max_count=1, start_timestamp="2000-01-01")
-    assert len(valid_result) == 1
-
-
-def test_serve_run_does_not_raise_exceptions(tmp_path: Path):
-    """Verify that serve() runs server.run without raise_exceptions=True."""
-    import anyio
-
-    repo_path = tmp_path / "serve_test_repo"
-    git.Repo.init(repo_path)
-
-    async def _run():
-        with mock.patch("mcp_server_git.server.stdio_server") as mock_stdio:
-            mock_read = mock.AsyncMock()
-            mock_write = mock.AsyncMock()
-            mock_stdio.return_value.__aenter__.return_value = (mock_read, mock_write)
-            mock_stdio.return_value.__aexit__.return_value = None
-
-            with mock.patch("mcp_server_git.server.Server.run", new_callable=mock.AsyncMock) as mock_run:
-                await serve(repo_path)
-                mock_run.assert_awaited_once()
-                _, kwargs = mock_run.call_args
-                assert kwargs.get("raise_exceptions") is not True
-
-    anyio.run(_run)

src/memory/README.md

@@ -72,7 +72,6 @@ Example:
       - `to` (string): Target entity name
       - `relationType` (string): Relationship type in active voice
   - Skips duplicate relations
-  - Fails if either the source or target entity doesn't exist
 
 - **add_observations**
   - Add new observations to existing entities
@@ -87,7 +86,7 @@ Example:
   - Remove entities and their relations
   - Input: `entityNames` (string[])
   - Cascading deletion of associated relations
-  - No error if an entity doesn't exist; the response reports which names were not found
+  - Silent operation if entity doesn't exist
 
 - **delete_observations**
   - Remove specific observations from entities
@@ -95,7 +94,7 @@ Example:
     - Each object contains:
       - `entityName` (string): Target entity
       - `observations` (string[]): Observations to remove
-  - No error if an observation doesn't exist; the response reports how many were deleted
+  - Silent operation if observation doesn't exist
 
 - **delete_relations**
   - Remove specific relations from the graph
@@ -104,7 +103,7 @@ Example:
       - `from` (string): Source entity name
       - `to` (string): Target entity name
       - `relationType` (string): Relationship type
-  - No error if a relation doesn't exist; the response reports how many were deleted
+  - Silent operation if relation doesn't exist
 
 - **read_graph**
   - Read the entire knowledge graph

src/memory/__tests__/delete-reporting.test.ts

@@ -1,99 +0,0 @@
-import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import { promises as fs } from 'fs';
-import path from 'path';
-import { fileURLToPath } from 'url';
-import { KnowledgeGraphManager, Entity, Relation } from '../index.js';
-
-/**
- * The delete tools stay silent when a target is absent, which the README
- * documents. What they must not do is report a deletion that did not happen:
- * an agent that mistypes a name is told its memory is clean while the data is
- * still on disk, and nothing in the response contradicts that.
- */
-describe('delete reporting', () => {
-  let manager: KnowledgeGraphManager;
-  let testFilePath: string;
-
-  const entities: Entity[] = [
-    { name: 'Alice', entityType: 'person', observations: ['works at Acme Corp', 'likes tea'] },
-    { name: 'Bob', entityType: 'person', observations: ['likes programming'] },
-  ];
-  const relations: Relation[] = [{ from: 'Alice', to: 'Bob', relationType: 'works_with' }];
-
-  beforeEach(async () => {
-    testFilePath = path.join(
-      path.dirname(fileURLToPath(import.meta.url)),
-      `test-delete-reporting-${Date.now()}-${Math.random().toString(16).slice(2)}.jsonl`
-    );
-    manager = new KnowledgeGraphManager(testFilePath);
-    await manager.createEntities(entities);
-    await manager.createRelations(relations);
-  });
-
-  afterEach(async () => {
-    try {
-      await fs.unlink(testFilePath);
-    } catch {
-      // the file is gone already
-    }
-  });
-
-  describe('deleteEntities', () => {
-    it('reports which names matched and which did not', async () => {
-      const result = await manager.deleteEntities(['Alice', 'Alise']);
-      expect(result).toEqual({ deleted: ['Alice'], notFound: ['Alise'] });
-    });
-
-    it('reports nothing deleted when no name matches', async () => {
-      const result = await manager.deleteEntities(['Nobody']);
-      expect(result).toEqual({ deleted: [], notFound: ['Nobody'] });
-
-      const graph = await manager.readGraph();
-      expect(graph.entities).toHaveLength(2);
-    });
-
-    it('still deletes the entity and its relations', async () => {
-      await manager.deleteEntities(['Alice']);
-
-      const graph = await manager.readGraph();
-      expect(graph.entities.map(e => e.name)).toEqual(['Bob']);
-      expect(graph.relations).toHaveLength(0);
-    });
-  });
-
-  describe('deleteObservations', () => {
-    it('counts only the observations that were present', async () => {
-      const result = await manager.deleteObservations([
-        { entityName: 'Alice', observations: ['likes tea', 'never said this'] },
-      ]);
-      expect(result).toEqual({ deletedCount: 1, missingEntities: [] });
-    });
-
-    it('names an entity that does not exist', async () => {
-      const result = await manager.deleteObservations([
-        { entityName: 'Carol', observations: ['anything'] },
-      ]);
-      expect(result).toEqual({ deletedCount: 0, missingEntities: ['Carol'] });
-    });
-  });
-
-  describe('deleteRelations', () => {
-    it('counts only the relations that matched', async () => {
-      const result = await manager.deleteRelations([
-        { from: 'Alice', to: 'Bob', relationType: 'works_with' },
-        { from: 'Alice', to: 'Bob', relationType: 'never_existed' },
-      ]);
-      expect(result).toEqual({ deletedCount: 1 });
-    });
-
-    it('reports nothing deleted when the relation type is wrong', async () => {
-      const result = await manager.deleteRelations([
-        { from: 'Alice', to: 'Bob', relationType: 'manages' },
-      ]);
-      expect(result).toEqual({ deletedCount: 0 });
-
-      const graph = await manager.readGraph();
-      expect(graph.relations).toHaveLength(1);
-    });
-  });
-});

src/memory/__tests__/file-path.test.ts

@@ -1,9 +1,8 @@
 import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
 import { promises as fs } from 'fs';
 import path from 'path';
-import os from 'os';
 import { fileURLToPath } from 'url';
-import { ensureMemoryFilePath, defaultMemoryPath, expandHome } from '../index.js';
+import { ensureMemoryFilePath, defaultMemoryPath } from '../index.js';
 
 describe('ensureMemoryFilePath', () => {
   const testDir = path.dirname(fileURLToPath(import.meta.url));
@@ -73,15 +72,6 @@ describe('ensureMemoryFilePath', () => {
         expect(path.isAbsolute(result)).toBe(true);
       }
     });
-
-    it('should expand a leading "~/" to the home directory', async () => {
-      process.env.MEMORY_FILE_PATH = '~/custom-memory.jsonl';
-
-      const result = await ensureMemoryFilePath();
-
-      expect(result).toBe(path.join(os.homedir(), 'custom-memory.jsonl'));
-      expect(path.isAbsolute(result)).toBe(true);
-    });
   });
 
   describe('without MEMORY_FILE_PATH environment variable', () => {
@@ -164,29 +154,3 @@ describe('ensureMemoryFilePath', () => {
     });
   });
 });
-
-describe('expandHome', () => {
-  it('expands a bare "~" to the home directory', () => {
-    expect(expandHome('~')).toBe(os.homedir());
-  });
-
-  it('expands a leading "~/" to the home directory', () => {
-    expect(expandHome('~/notes/memory.jsonl')).toBe(
-      path.join(os.homedir(), 'notes/memory.jsonl')
-    );
-  });
-
-  it('leaves a "~" not followed by a separator unchanged', () => {
-    expect(expandHome('~backup.jsonl')).toBe('~backup.jsonl');
-  });
-
-  it('leaves absolute paths unchanged', () => {
-    expect(expandHome('/var/data/memory.jsonl')).toBe('/var/data/memory.jsonl');
-  });
-
-  it('leaves relative paths unchanged', () => {
-    expect(expandHome(path.join('data', 'memory.jsonl'))).toBe(
-      path.join('data', 'memory.jsonl')
-    );
-  });
-});

src/memory/__tests__/knowledge-graph.test.ts

@@ -59,20 +59,6 @@ describe('KnowledgeGraphManager', () => {
       const newEntities = await manager.createEntities([]);
       expect(newEntities).toHaveLength(0);
     });
-
-    it('should ignore duplicate entity names within a single batch', async () => {
-      const entities: Entity[] = [
-        { name: 'Alice', entityType: 'person', observations: ['first'] },
-        { name: 'Alice', entityType: 'person', observations: ['second'] },
-      ];
-
-      const newEntities = await manager.createEntities(entities);
-      expect(newEntities).toHaveLength(1);
-
-      const graph = await manager.readGraph();
-      expect(graph.entities).toHaveLength(1);
-      expect(graph.entities[0].name).toBe('Alice');
-    });
   });
 
   describe('createRelations', () => {
@@ -113,60 +99,10 @@ describe('KnowledgeGraphManager', () => {
       expect(graph.relations).toHaveLength(1);
     });
 
-    it('should reject relations from non-existent entities', async () => {
-      await manager.createEntities([
-        { name: 'Alice', entityType: 'person', observations: [] },
-      ]);
-
-      await expect(
-        manager.createRelations([
-          { from: 'Ghost', to: 'Alice', relationType: 'knows' },
-        ])
-      ).rejects.toThrow('Entity with name Ghost not found');
-
-      const graph = await manager.readGraph();
-      expect(graph.relations).toHaveLength(0);
-    });
-
-    it('should reject relation batches that reference non-existent target entities', async () => {
-      await manager.createEntities([
-        { name: 'Alice', entityType: 'person', observations: [] },
-        { name: 'Bob', entityType: 'person', observations: [] },
-      ]);
-
-      await expect(
-        manager.createRelations([
-          { from: 'Alice', to: 'Bob', relationType: 'knows' },
-          { from: 'Alice', to: 'Ghost', relationType: 'knows' },
-        ])
-      ).rejects.toThrow('Entity with name Ghost not found');
-
-      const graph = await manager.readGraph();
-      expect(graph.relations).toHaveLength(0);
-    });
-
     it('should handle empty relation arrays', async () => {
       const newRelations = await manager.createRelations([]);
       expect(newRelations).toHaveLength(0);
     });
-
-    it('should skip duplicate relations within a single batch', async () => {
-      await manager.createEntities([
-        { name: 'Alice', entityType: 'person', observations: [] },
-        { name: 'Bob', entityType: 'person', observations: [] },
-      ]);
-
-      const relations: Relation[] = [
-        { from: 'Alice', to: 'Bob', relationType: 'knows' },
-        { from: 'Alice', to: 'Bob', relationType: 'knows' },
-      ];
-
-      const newRelations = await manager.createRelations(relations);
-      expect(newRelations).toHaveLength(1);
-
-      const graph = await manager.readGraph();
-      expect(graph.relations).toHaveLength(1);
-    });
   });
 
   describe('addObservations', () => {
@@ -210,11 +146,11 @@ describe('KnowledgeGraphManager', () => {
     });
 
     it('should throw error for non-existent entity', async () => {
-      await expect(async () => {
-        await manager.addObservations([
+      await expect(
+        manager.addObservations([
           { entityName: 'NonExistent', contents: ['some observation'] },
-        ]);
-      }).rejects.toThrow('Entity with name NonExistent not found');
+        ])
+      ).rejects.toThrow('Entity with name NonExistent not found');
     });
   });
 
@@ -490,76 +426,6 @@ describe('KnowledgeGraphManager', () => {
       expect(JSON.parse(lines[1])).toHaveProperty('type', 'relation');
     });
 
-    it('should write a trailing newline to produce valid JSONL', async () => {
-      await manager.createEntities([
-        { name: 'Alice', entityType: 'person', observations: ['test'] },
-      ]);
-
-      const fileContent = await fs.readFile(testFilePath, 'utf-8');
-      expect(fileContent.endsWith('\n')).toBe(true);
-    });
-
-    it('should produce a file where every line is individually valid JSON', async () => {
-      // This test catches the bug where saveGraph wrote lines.join("\n")
-      // without a trailing newline. When the file was later appended to
-      // (e.g. by a concurrent process or external tool), the last JSON
-      // object and the new first JSON object ended up on the same line,
-      // producing invalid JSONL like:
-      //   {"type":"entity","name":"Alice"}{"type":"relation","from":"Alice",...}
-      // which fails with: "Unexpected non-whitespace character after JSON
-      // at position N"
-      await manager.createEntities([
-        { name: 'Alice', entityType: 'person', observations: ['test'] },
-        { name: 'Bob', entityType: 'person', observations: [] },
-      ]);
-      await manager.createRelations([
-        { from: 'Alice', to: 'Bob', relationType: 'knows' },
-      ]);
-
-      const fileContent = await fs.readFile(testFilePath, 'utf-8');
-      const allLines = fileContent.split('\n');
-
-      // Every non-empty line must be valid JSON on its own
-      for (const line of allLines) {
-        if (line.trim() === '') continue;
-        expect(() => JSON.parse(line)).not.toThrow();
-      }
-    });
-
-    it('should not corrupt JSONL when content is appended to the file externally', async () => {
-      // Simulate the real-world corruption scenario:
-      // 1. saveGraph writes entities to the file
-      // 2. An external process appends a new JSON line to the file
-      // 3. loadGraph must still parse the file without errors
-      //
-      // Without a trailing newline on step 1, the appended content in
-      // step 2 lands on the same line as the last entity, producing
-      // invalid JSONL that breaks loadGraph.
-      await manager.createEntities([
-        { name: 'Alice', entityType: 'person', observations: ['original'] },
-      ]);
-
-      // Simulate an external append (e.g. another process, a script, or
-      // a crash-recovery replay). This is what triggers the bug: without
-      // a trailing newline, this JSON object concatenates onto line 1.
-      const externalLine = JSON.stringify({
-        type: 'entity',
-        name: 'External',
-        entityType: 'person',
-        observations: ['appended externally'],
-      });
-      await fs.appendFile(testFilePath, externalLine + '\n');
-
-      // A new manager instance forces a fresh loadGraph from disk
-      const manager2 = new KnowledgeGraphManager(testFilePath);
-      const graph = await manager2.readGraph();
-
-      // Both entities must load without a JSON parse error
-      expect(graph.entities).toHaveLength(2);
-      expect(graph.entities.map(e => e.name)).toContain('Alice');
-      expect(graph.entities.map(e => e.name)).toContain('External');
-    });
-
     it('should strip type field from entities when loading from file', async () => {
       // Create entities and relations (these get saved with type field)
       await manager.createEntities([
@@ -649,126 +515,4 @@ describe('KnowledgeGraphManager', () => {
       expect(result.relations[0]).not.toHaveProperty('type');
     });
   });
-
-  describe('loadGraph validation', () => {
-    it('skips corrupt entities instead of crashing search', async () => {
-      const lines = [
-        JSON.stringify({ type: 'entity', name: 'Alice', entityType: 'person', observations: ['works at Acme Corp'] }),
-        JSON.stringify({ type: 'entity', name: 'Broken', observations: ['missing entityType'] }),
-        JSON.stringify({ type: 'entity', name: 'BadObs', entityType: 'person', observations: ['ok', null] }),
-      ];
-      await fs.writeFile(testFilePath, lines.join('\n') + '\n');
-
-      const graph = await manager.readGraph();
-      expect(graph.entities).toHaveLength(1);
-      expect(graph.entities[0].name).toBe('Alice');
-
-      // searchNodes must not throw even though the file contains corrupt entries
-      const result = await manager.searchNodes('Acme');
-      expect(result.entities).toHaveLength(1);
-      expect(result.entities[0].name).toBe('Alice');
-    });
-
-    it('skips corrupt relations', async () => {
-      const lines = [
-        JSON.stringify({ type: 'entity', name: 'Alice', entityType: 'person', observations: [] }),
-        JSON.stringify({ type: 'relation', from: 'Alice', to: 'Bob' }), // missing relationType
-        JSON.stringify({ type: 'relation', from: 'Alice', to: 'Bob', relationType: 'knows' }),
-      ];
-      await fs.writeFile(testFilePath, lines.join('\n') + '\n');
-
-      const graph = await manager.readGraph();
-      expect(graph.entities).toHaveLength(1);
-      expect(graph.relations).toHaveLength(1);
-      expect(graph.relations[0].relationType).toBe('knows');
-    });
-
-    it('skips malformed JSON lines', async () => {
-      const lines = [
-        JSON.stringify({ type: 'entity', name: 'Alice', entityType: 'person', observations: [] }),
-        '{this is not valid json',
-        JSON.stringify({ type: 'entity', name: 'Bob', entityType: 'person', observations: [] }),
-      ];
-      await fs.writeFile(testFilePath, lines.join('\n') + '\n');
-
-      const graph = await manager.readGraph();
-      expect(graph.entities).toHaveLength(2);
-      expect(graph.entities.map(e => e.name)).toEqual(['Alice', 'Bob']);
-    });
-  });
-
-  describe('concurrent mutations', () => {
-    // Regression test for #1819: concurrent tool calls each independently
-    // load the graph, mutate their own copy, and write it back. Without
-    // serialization, whichever write lands last silently discards the
-    // other's changes. All mutations below are fired without awaiting each
-    // other first, simulating multiple tool calls landing close together.
-
-    it('should not lose entities created concurrently', async () => {
-      const batch1: Entity[] = Array.from({ length: 10 }, (_, i) => ({
-        name: `batch1-entity-${i}`,
-        entityType: 'test',
-        observations: [],
-      }));
-      const batch2: Entity[] = Array.from({ length: 10 }, (_, i) => ({
-        name: `batch2-entity-${i}`,
-        entityType: 'test',
-        observations: [],
-      }));
-
-      // Fire both concurrently instead of awaiting sequentially.
-      await Promise.all([
-        manager.createEntities(batch1),
-        manager.createEntities(batch2),
-      ]);
-
-      const graph = await manager.readGraph();
-      expect(graph.entities).toHaveLength(20);
-      expect(graph.entities.map(e => e.name).sort()).toEqual(
-        [...batch1, ...batch2].map(e => e.name).sort()
-      );
-    });
-
-    it('should not lose relations created concurrently with entity creation', async () => {
-      await manager.createEntities([
-        { name: 'Alice', entityType: 'person', observations: [] },
-        { name: 'Bob', entityType: 'person', observations: [] },
-        { name: 'Carol', entityType: 'person', observations: [] },
-      ]);
-
-      await Promise.all([
-        manager.createRelations([{ from: 'Alice', to: 'Bob', relationType: 'knows' }]),
-        manager.createRelations([{ from: 'Bob', to: 'Carol', relationType: 'knows' }]),
-        manager.addObservations([
-          { entityName: 'Alice', contents: ['likes coffee'] },
-        ]),
-      ]);
-
-      const graph = await manager.readGraph();
-      expect(graph.relations).toHaveLength(2);
-      expect(graph.entities.find(e => e.name === 'Alice')?.observations).toContain('likes coffee');
-    });
-
-    it('should keep the file valid JSONL after many concurrent mutations', async () => {
-      const operations = Array.from({ length: 25 }, (_, i) =>
-        manager.createEntities([
-          { name: `stress-entity-${i}`, entityType: 'test', observations: [] },
-        ])
-      );
-
-      await Promise.all(operations);
-
-      const raw = await fs.readFile(testFilePath, 'utf-8');
-      const lines = raw.split('\n').filter(line => line.trim() !== '');
-
-      // Every line must parse as valid JSON; a corrupted interleaved write
-      // would produce a truncated or malformed line here.
-      for (const line of lines) {
-        expect(() => JSON.parse(line)).not.toThrow();
-      }
-
-      const graph = await manager.readGraph();
-      expect(graph.entities).toHaveLength(25);
-    });
-  });
 });

src/memory/__tests__/search-nodes-schema.test.ts

@@ -1,25 +0,0 @@
-import { describe, it, expect } from 'vitest';
-import { SearchNodesQuerySchema, SEARCH_QUERY_MAX_LENGTH } from '../index.js';
-
-describe('search_nodes input schema', () => {
-  it('should accept a normal query', () => {
-    expect(SearchNodesQuerySchema.safeParse('Alice').success).toBe(true);
-    expect(SearchNodesQuerySchema.safeParse('works at Acme Corp').success).toBe(true);
-  });
-
-  it('should accept a query at exactly the max length', () => {
-    const atLimit = 'a'.repeat(SEARCH_QUERY_MAX_LENGTH);
-    expect(SearchNodesQuerySchema.safeParse(atLimit).success).toBe(true);
-  });
-
-  it('should reject a query longer than the max length', () => {
-    const oversized = 'a'.repeat(SEARCH_QUERY_MAX_LENGTH + 1);
-    const result = SearchNodesQuerySchema.safeParse(oversized);
-    expect(result.success).toBe(false);
-  });
-
-  it('should still reject non-string input', () => {
-    expect(SearchNodesQuerySchema.safeParse(42).success).toBe(false);
-    expect(SearchNodesQuerySchema.safeParse(null).success).toBe(false);
-  });
-});

src/memory/__tests__/server-version.test.ts

@@ -1,25 +0,0 @@
-import { describe, it, expect } from 'vitest';
-import { createRequire } from 'node:module';
-import path from 'path';
-import { fileURLToPath } from 'url';
-import { resolvePackageVersion, SERVER_VERSION } from '../version.js';
-
-const packageJson = createRequire(import.meta.url)('../package.json') as { version: string };
-
-describe('server version', () => {
-  it('uses package.json version for serverInfo', () => {
-    expect(SERVER_VERSION).toBe(packageJson.version);
-    expect(resolvePackageVersion()).toBe(packageJson.version);
-  });
-
-  it('resolves package.json from the dist layout', () => {
-    const distDir = path.join(path.dirname(fileURLToPath(import.meta.url)), '..', 'dist');
-    const distVersionPath = path.join(distDir, 'version.js');
-
-    expect(() => createRequire(distVersionPath)('./version.js')).not.toThrow();
-    const distModule = createRequire(distVersionPath)('./version.js') as {
-      SERVER_VERSION: string;
-    };
-    expect(distModule.SERVER_VERSION).toBe(packageJson.version);
-  });
-});

src/memory/index.ts

@@ -6,35 +6,19 @@ import { SubscribeRequestSchema, UnsubscribeRequestSchema } from "@modelcontextp
 import { z } from "zod";
 import { promises as fs } from 'fs';
 import path from 'path';
-import os from 'os';
 import { randomBytes } from 'crypto';
 import { fileURLToPath } from 'url';
-import { SERVER_VERSION } from './version.js';
 
 // Define memory file path using environment variable with fallback
 export const defaultMemoryPath = path.join(path.dirname(fileURLToPath(import.meta.url)), 'memory.jsonl');
 
-// Expand a leading "~" to the user's home directory. MCP clients pass
-// MEMORY_FILE_PATH from JSON config, where no shell performs tilde expansion,
-// so an unexpanded "~" would otherwise be treated as a relative path and
-// joined onto the package directory. Mirrors the helper of the same name in
-// the filesystem server (src/filesystem/path-utils.ts).
-export function expandHome(filepath: string): string {
-  if (filepath.startsWith('~/') || filepath === '~') {
-    return path.join(os.homedir(), filepath.slice(1));
-  }
-  return filepath;
-}
-
 // Handle backward compatibility: migrate memory.json to memory.jsonl if needed
 export async function ensureMemoryFilePath(): Promise<string> {
   if (process.env.MEMORY_FILE_PATH) {
-    // Custom path provided. Expand a leading "~" first, then resolve relative
-    // paths against the package directory (absolute paths are used as-is).
-    const customPath = expandHome(process.env.MEMORY_FILE_PATH);
-    return path.isAbsolute(customPath)
-      ? customPath
-      : path.join(path.dirname(fileURLToPath(import.meta.url)), customPath);
+    // Custom path provided, use it as-is (with absolute path resolution)
+    return path.isAbsolute(process.env.MEMORY_FILE_PATH)
+      ? process.env.MEMORY_FILE_PATH
+      : path.join(path.dirname(fileURLToPath(import.meta.url)), process.env.MEMORY_FILE_PATH);
   }
   
   // No custom path set, check for backward compatibility migration
@@ -86,71 +70,28 @@ export interface KnowledgeGraph {
 export class KnowledgeGraphManager {
   constructor(private memoryFilePath: string) {}
 
-  // Serializes all read-modify-write graph mutations behind a single queue.
-  // Without this, concurrent tool calls (e.g. multiple mutations dispatched
-  // from one LLM turn) each independently load the graph, mutate their own
-  // copy, and write it back — so whichever write lands last silently
-  // overwrites the other's changes, and interleaved writes to the same file
-  // can corrupt it outright. See #1819.
-  private mutationQueue: Promise<unknown> = Promise.resolve();
-
-  private async withLock<T>(operation: () => Promise<T>): Promise<T> {
-    const result = this.mutationQueue.then(operation, operation);
-    // Always resolve the queue itself, even if this operation failed, so a
-    // single failed mutation doesn't permanently wedge every call after it.
-    // The failure still propagates normally to whoever awaited `result`.
-    this.mutationQueue = result.then(
-      () => undefined,
-      () => undefined,
-    );
-    return result;
-  }
-
   private async loadGraph(): Promise<KnowledgeGraph> {
     try {
       const data = await fs.readFile(this.memoryFilePath, "utf-8");
       const lines = data.split("\n").filter(line => line.trim() !== "");
-      const graph: KnowledgeGraph = { entities: [], relations: [] };
-
-      for (const line of lines) {
-        let item: unknown;
-        try {
-          item = JSON.parse(line);
-        } catch {
-          console.error("Skipping malformed line in memory file");
-          continue;
+      return lines.reduce((graph: KnowledgeGraph, line) => {
+        const item = JSON.parse(line);
+        if (item.type === "entity") {
+          graph.entities.push({
+            name: item.name,
+            entityType: item.entityType,
+            observations: item.observations
+          });
         }
-
-        if (typeof item !== "object" || item === null) {
-          console.error("Skipping non-object line in memory file");
-          continue;
+        if (item.type === "relation") {
+          graph.relations.push({
+            from: item.from,
+            to: item.to,
+            relationType: item.relationType
+          });
         }
-
-        const record = item as Record<string, unknown>;
-        if (record.type === "entity") {
-          const parsed = EntitySchema.safeParse(item);
-          if (parsed.success) {
-            graph.entities.push(parsed.data);
-          } else {
-            console.error(
-              "Skipping invalid entity in memory file:",
-              parsed.error.issues.map(issue => `${issue.path.join(".")}: ${issue.message}`).join(", ")
-            );
-          }
-        } else if (record.type === "relation") {
-          const parsed = RelationSchema.safeParse(item);
-          if (parsed.success) {
-            graph.relations.push(parsed.data);
-          } else {
-            console.error(
-              "Skipping invalid relation in memory file:",
-              parsed.error.issues.map(issue => `${issue.path.join(".")}: ${issue.message}`).join(", ")
-            );
-          }
-        }
-      }
-
-      return graph;
+        return graph;
+      }, { entities: [], relations: [] });
     } catch (error) {
       if (error instanceof Error && 'code' in error && (error as any).code === "ENOENT") {
         return { entities: [], relations: [] };
@@ -190,7 +131,7 @@ export class KnowledgeGraphManager {
     );
 
     try {
-      await fs.writeFile(tempFilePath, lines.join("\n") + "\n");
+      await fs.writeFile(tempFilePath, lines.join("\n"));
       await fs.rename(tempFilePath, this.memoryFilePath);
     } catch (error) {
       // Never leave a stray temp file behind on failure.
@@ -200,110 +141,66 @@ export class KnowledgeGraphManager {
   }
 
   async createEntities(entities: Entity[]): Promise<Entity[]> {
-    return this.withLock(async () => {
-      const graph = await this.loadGraph();
-      const newEntities = entities.filter((e, index) =>
-        !graph.entities.some(existingEntity => existingEntity.name === e.name) &&
-        // Also skip duplicates appearing earlier in this same batch
-        !entities.slice(0, index).some(earlier => earlier.name === e.name)
-      );
-      graph.entities.push(...newEntities);
-      await this.saveGraph(graph);
-      return newEntities;
-    });
+    const graph = await this.loadGraph();
+    const newEntities = entities.filter(e => !graph.entities.some(existingEntity => existingEntity.name === e.name));
+    graph.entities.push(...newEntities);
+    await this.saveGraph(graph);
+    return newEntities;
   }
 
   async createRelations(relations: Relation[]): Promise<Relation[]> {
-    return this.withLock(async () => {
-      const graph = await this.loadGraph();
-      const entityNames = new Set(graph.entities.map(e => e.name));
-
-      relations.forEach(r => {
-        if (!entityNames.has(r.from)) {
-          throw new Error(`Entity with name ${r.from} not found`);
-        }
-        if (!entityNames.has(r.to)) {
-          throw new Error(`Entity with name ${r.to} not found`);
-        }
-      });
-
-      const isSameRelation = (a: Relation, b: Relation) =>
-        a.from === b.from &&
-        a.to === b.to &&
-        a.relationType === b.relationType;
-      const newRelations = relations.filter((r, index) =>
-        !graph.relations.some(existingRelation => isSameRelation(existingRelation, r)) &&
-        // Also skip duplicates appearing earlier in this same batch
-        !relations.slice(0, index).some(earlier => isSameRelation(earlier, r))
-      );
-      graph.relations.push(...newRelations);
-      await this.saveGraph(graph);
-      return newRelations;
-    });
+    const graph = await this.loadGraph();
+    const newRelations = relations.filter(r => !graph.relations.some(existingRelation => 
+      existingRelation.from === r.from && 
+      existingRelation.to === r.to && 
+      existingRelation.relationType === r.relationType
+    ));
+    graph.relations.push(...newRelations);
+    await this.saveGraph(graph);
+    return newRelations;
   }
 
   async addObservations(observations: { entityName: string; contents: string[] }[]): Promise<{ entityName: string; addedObservations: string[] }[]> {
-    return this.withLock(async () => {
-      const graph = await this.loadGraph();
-      const results = observations.map(o => {
-        const entity = graph.entities.find(e => e.name === o.entityName);
-        if (!entity) {
-          throw new Error(`Entity with name ${o.entityName} not found`);
-        }
-        const newObservations = o.contents.filter(content => !entity.observations.includes(content));
-        entity.observations.push(...newObservations);
-        return { entityName: o.entityName, addedObservations: newObservations };
-      });
-      await this.saveGraph(graph);
-      return results;
+    const graph = await this.loadGraph();
+    const results = observations.map(o => {
+      const entity = graph.entities.find(e => e.name === o.entityName);
+      if (!entity) {
+        throw new Error(`Entity with name ${o.entityName} not found`);
+      }
+      const newObservations = o.contents.filter(content => !entity.observations.includes(content));
+      entity.observations.push(...newObservations);
+      return { entityName: o.entityName, addedObservations: newObservations };
     });
+    await this.saveGraph(graph);
+    return results;
   }
 
-  async deleteEntities(entityNames: string[]): Promise<{ deleted: string[]; notFound: string[] }> {
-    return this.withLock(async () => {
-      const graph = await this.loadGraph();
-      const present = new Set(graph.entities.map(e => e.name));
-      const deleted = entityNames.filter(name => present.has(name));
-      const notFound = entityNames.filter(name => !present.has(name));
-      graph.entities = graph.entities.filter(e => !entityNames.includes(e.name));
-      graph.relations = graph.relations.filter(r => !entityNames.includes(r.from) && !entityNames.includes(r.to));
-      await this.saveGraph(graph);
-      return { deleted, notFound };
-    });
+  async deleteEntities(entityNames: string[]): Promise<void> {
+    const graph = await this.loadGraph();
+    graph.entities = graph.entities.filter(e => !entityNames.includes(e.name));
+    graph.relations = graph.relations.filter(r => !entityNames.includes(r.from) && !entityNames.includes(r.to));
+    await this.saveGraph(graph);
   }
 
-  async deleteObservations(deletions: { entityName: string; observations: string[] }[]): Promise<{ deletedCount: number; missingEntities: string[] }> {
-    return this.withLock(async () => {
-      const graph = await this.loadGraph();
-      let deletedCount = 0;
-      const missingEntities: string[] = [];
-      deletions.forEach(d => {
-        const entity = graph.entities.find(e => e.name === d.entityName);
-        if (entity) {
-          const before = entity.observations.length;
-          entity.observations = entity.observations.filter(o => !d.observations.includes(o));
-          deletedCount += before - entity.observations.length;
-        } else {
-          missingEntities.push(d.entityName);
-        }
-      });
-      await this.saveGraph(graph);
-      return { deletedCount, missingEntities };
+  async deleteObservations(deletions: { entityName: string; observations: string[] }[]): Promise<void> {
+    const graph = await this.loadGraph();
+    deletions.forEach(d => {
+      const entity = graph.entities.find(e => e.name === d.entityName);
+      if (entity) {
+        entity.observations = entity.observations.filter(o => !d.observations.includes(o));
+      }
     });
+    await this.saveGraph(graph);
   }
 
-  async deleteRelations(relations: Relation[]): Promise<{ deletedCount: number }> {
-    return this.withLock(async () => {
-      const graph = await this.loadGraph();
-      const before = graph.relations.length;
-      graph.relations = graph.relations.filter(r => !relations.some(delRelation => 
-        r.from === delRelation.from && 
-        r.to === delRelation.to && 
-        r.relationType === delRelation.relationType
-      ));
-      await this.saveGraph(graph);
-      return { deletedCount: before - graph.relations.length };
-    });
+  async deleteRelations(relations: Relation[]): Promise<void> {
+    const graph = await this.loadGraph();
+    graph.relations = graph.relations.filter(r => !relations.some(delRelation => 
+      r.from === delRelation.from && 
+      r.to === delRelation.to && 
+      r.relationType === delRelation.relationType
+    ));
+    await this.saveGraph(graph);
   }
 
   async readGraph(): Promise<KnowledgeGraph> {
@@ -379,9 +276,10 @@ const RelationSchema = z.object({
   relationType: z.string().describe("The type of the relation")
 });
 
+// The server instance and tools exposed to Claude
 const server = new McpServer({
   name: "memory-server",
-  version: SERVER_VERSION,
+  version: "0.6.3",
 });
 
 const RESOURCE_URI = "memory://knowledge-graph";
@@ -512,14 +410,11 @@ server.registerTool(
     }
   },
   async ({ entityNames }) => {
-    const { deleted, notFound } = await knowledgeGraphManager.deleteEntities(entityNames);
+    await knowledgeGraphManager.deleteEntities(entityNames);
     notifyGraphUpdated();
-    const message = notFound.length === 0
-      ? "Entities deleted successfully"
-      : `Deleted ${deleted.length} of ${entityNames.length} entities. Not found: ${notFound.join(", ")}`;
     return {
-      content: [{ type: "text" as const, text: message }],
-      structuredContent: { success: true, message }
+      content: [{ type: "text" as const, text: "Entities deleted successfully" }],
+      structuredContent: { success: true, message: "Entities deleted successfully" }
     };
   }
 );
@@ -548,16 +443,11 @@ server.registerTool(
     }
   },
   async ({ deletions }) => {
-    const { deletedCount, missingEntities } = await knowledgeGraphManager.deleteObservations(deletions);
+    await knowledgeGraphManager.deleteObservations(deletions);
     notifyGraphUpdated();
-    const requested = deletions.reduce((total, d) => total + d.observations.length, 0);
-    const message = deletedCount === requested
-      ? "Observations deleted successfully"
-      : `Deleted ${deletedCount} of ${requested} observations.` +
-        (missingEntities.length ? ` Entities not found: ${missingEntities.join(", ")}` : "");
     return {
-      content: [{ type: "text" as const, text: message }],
-      structuredContent: { success: true, message }
+      content: [{ type: "text" as const, text: "Observations deleted successfully" }],
+      structuredContent: { success: true, message: "Observations deleted successfully" }
     };
   }
 );
@@ -583,14 +473,11 @@ server.registerTool(
     }
   },
   async ({ relations }) => {
-    const { deletedCount } = await knowledgeGraphManager.deleteRelations(relations);
+    await knowledgeGraphManager.deleteRelations(relations);
     notifyGraphUpdated();
-    const message = deletedCount === relations.length
-      ? "Relations deleted successfully"
-      : `Deleted ${deletedCount} of ${relations.length} relations. The rest matched nothing.`;
     return {
-      content: [{ type: "text" as const, text: message }],
-      structuredContent: { success: true, message }
+      content: [{ type: "text" as const, text: "Relations deleted successfully" }],
+      structuredContent: { success: true, message: "Relations deleted successfully" }
     };
   }
 );
@@ -622,13 +509,6 @@ server.registerTool(
   }
 );
 
-export const SEARCH_QUERY_MAX_LENGTH = 2048;
-
-export const SearchNodesQuerySchema = z
-  .string()
-  .max(SEARCH_QUERY_MAX_LENGTH)
-  .describe("The search query to match against entity names, types, and observation content");
-
 // Register search_nodes tool
 server.registerTool(
   "search_nodes",
@@ -636,7 +516,7 @@ server.registerTool(
     title: "Search Nodes",
     description: "Search for nodes in the knowledge graph based on a query",
     inputSchema: {
-      query: SearchNodesQuerySchema
+      query: z.string().describe("The search query to match against entity names, types, and observation content")
     },
     outputSchema: {
       entities: z.array(EntitySchema),

src/memory/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@modelcontextprotocol/server-memory",
-  "version": "0.6.3",
+  "version": "2026.8.31",
   "description": "MCP server for enabling memory for Claude through a knowledge graph",
   "license": "SEE LICENSE IN LICENSE",
   "mcpName": "io.github.modelcontextprotocol/server-memory",
@@ -25,8 +25,7 @@
     "test": "vitest run --coverage"
   },
   "dependencies": {
-    "@modelcontextprotocol/sdk": "^1.30.0",
-    "zod": "^4.0.0"
+    "@modelcontextprotocol/sdk": "^1.30.0"
   },
   "devDependencies": {
     "@types/node": "^22",

src/memory/version.ts

@@ -1,27 +0,0 @@
-import { createRequire } from 'node:module';
-import path from 'path';
-import { fileURLToPath } from 'url';
-
-export function resolvePackageVersion(): string {
-  const require = createRequire(import.meta.url);
-  const moduleDir = path.dirname(fileURLToPath(import.meta.url));
-  const candidates = [
-    path.join(moduleDir, 'package.json'),
-    path.join(moduleDir, '..', 'package.json'),
-  ];
-
-  for (const candidate of candidates) {
-    try {
-      const pkg = require(candidate) as { version?: string };
-      if (pkg.version) {
-        return pkg.version;
-      }
-    } catch {
-      // Try the next candidate when running from dist/ or source.
-    }
-  }
-
-  throw new Error('Could not locate package.json for server version');
-}
-
-export const SERVER_VERSION = resolvePackageVersion();

src/sequentialthinking/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@modelcontextprotocol/server-sequential-thinking",
-  "version": "0.6.2",
+  "version": "2026.8.31",
   "description": "MCP server for sequential thinking and problem solving",
   "license": "SEE LICENSE IN LICENSE",
   "mcpName": "io.github.modelcontextprotocol/server-sequential-thinking",
@@ -27,8 +27,7 @@
   "dependencies": {
     "@modelcontextprotocol/sdk": "^1.30.0",
     "chalk": "^5.3.0",
-    "yargs": "^17.7.2",
-    "zod": "^4.0.0"
+    "yargs": "^17.7.2"
   },
   "devDependencies": {
     "@types/node": "^22",
@@ -38,4 +37,4 @@
     "typescript": "^5.3.3",
     "vitest": "^4.1.8"
   }
-}
+}