Filesystem extension: Frequent timeout or outright failures since claude desktop 1.1.1520

Describe the bug
For the last three days I have been having frequent timeouts where any sort of filesystem extension activity results in either a delay of minutes before it resolves or the claude desktop app just gives up entirely and deletes the last few chat messages. I also get frequent messages where the edits that it attempts to make are failed. Nothing has changed in my setup and it worked great for the last two weeks before this.

Logs

2026-02-01T15:29:43.550Z [Filesystem] [info] Initializing server... { metadata: undefined }
2026-02-01T15:29:43.607Z [Filesystem] [info] Using built-in Node.js for MCP server: Filesystem { metadata: undefined }
2026-02-01T15:29:43.636Z [Filesystem] [info] Server started and connected successfully { metadata: undefined }
2026-02-01T15:29:43.870Z [Filesystem] [info] Message from client: {"method":"initialize","params":{"protocolVersion":"2025-06-18","capabilities":{},"clientInfo":{"name":"claude-ai","version":"0.1.0"}},"jsonrpc":"2.0","id":0} { metadata: undefined }
2026-02-01T15:30:03.229Z [Filesystem] [info] Message from server: {"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"secure-filesystem-server","version":"0.2.0"}},"jsonrpc":"2.0","id":0} { metadata: undefined }
2026-02-01T15:30:03.231Z [Filesystem] [info] Message from client: {"method":"notifications/initialized","jsonrpc":"2.0"} { metadata: undefined }
2026-02-01T15:30:03.232Z [Filesystem] [info] Message from client: {"method":"tools/list","params":{},"jsonrpc":"2.0","id":1} { metadata: undefined }
2026-02-01T15:30:03.241Z [Filesystem] [info] Message from server: {"result":{"tools":[{"name":"read_file","description":"Read the complete contents of a file as text. DEPRECATED: Use read_text_file instead.","inputSchema":{"type":"object","properties":{"path":{"type":"string"},"tail":{"type":"number","description":"If pr...[7463 chars truncated]...ies within these allowed directories are also accessible. Use this to understand which directories and their nested paths are available before trying to access files.","inputSchema":{"type":"object","properties":{},"required":[]}}]},"jsonrpc":"2.0","id":1} { metadata: undefined }
2026-02-01T15:32:27.000Z [Filesystem] [info] Message from client: {"method":"tools/call","params":{"name":"write_file","arguments":{"path":"C:\prj\claude\JIGSAW_GAME_DESIGN_BACKUP.md","content":"# Jigsaw Puzzle Game - Design Document\nStatus: Phase 2 Complete | Updated: 2025-02-01\n\n## Project Overview\n\nA stand...[15203 chars truncated]...uzzle.html?image=${encodeURIComponent(imageFile)}&level=${level}&multiplier=${multiplier}`;\n// Result: puzzle.html?image=images%2Falpine%20meadow---ytiles%3D10%20bcolor%3D00000%20wcolor%3Daa0000.jpg&level=1&multiplier=1.0\n```\n"}},"jsonrpc":"2.0","id":2} { metadata: undefined }
2026-02-01T15:32:27.047Z [Filesystem] [info] Message from server: {"result":{"content":[{"type":"text","text":"Successfully wrote to C:\prj\claude\JIGSAW_GAME_DESIGN_BACKUP.md"}]},"jsonrpc":"2.0","id":2} { metadata: undefined }

Start with the filesystem extension's initialize, tools/list, and write_file exchanges shown in the logs, then reproduce the behavior in Claude Desktop 1.1.1520. Compare successful and failing filesystem calls, including the reported timeouts and failed edits. The issue is done when filesystem operations complete reliably without timeouts, failed edits, or lost chat messages.