[BUG] Claude Desktop (Windows): tools/call never dispatched to filesystem MCP server after successful handshake — persists across all transports, server versions, and full reinstall

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

On Claude Desktop for Windows (MSIX build 1.24012.1.0, installed at C:\Program Files\WindowsApps\Claude_1.24012.1.0_x64__pzs8sxrjxfjjc), the @modelcontextprotocol/server-filesystem MCP server completes the full handshake (initialize → tools/list) successfully, but tools/call messages are never dispatched by the client. The UI immediately shows Failed to call tool "...", and the failed calls leave no trace whatsoever in the server logs — the server never receives them.

This setup worked flawlessly on 2026-07-18/19 (20+ successful tools/call round-trips confirmed in mcp-server-files.log). It broke by 2026-07-22 with no configuration change on my side, which matches the auto-update window of the Desktop app.

Meanwhile, two other MCP servers configured in the same claude_desktop_config.json (Obsidian Local REST API, connected via npx mcp-remote over localhost HTTP) continue to work perfectly in the same chat sessions. Only the filesystem server is affected.

What Should Happen?

After a successful handshake, tools/call should be dispatched to the server, as it was until 2026-07-19.

Error Messages/Logs

**`mcp-server-files.log`** — identical pattern on every session since 07-22:
 

2026-07-22T13:09:26.233Z [files] [info] Server started and connected successfully
2026-07-22T13:09:26.692Z [files] [info] Message from client: method="initialize" id=0
2026-07-22T13:09:26.704Z [files] [info] Message from server: id=0 result
2026-07-22T13:09:26.978Z [files] [info] Message from client: method="notifications/initialized"
2026-07-22T13:09:26.979Z [files] [info] Message from client: method="tools/list" id=1
2026-07-22T13:09:26.983Z [files] [info] Message from server: id=1 result
// ← NOTHING after this. tools/call requested repeatedly from chat; none ever arrive.

 
For comparison, the same log on **2026-07-18** shows `tools/call` id=2 through id=20+ all succeeding within milliseconds, over more than an hour of use — ruling out any "first N seconds only" window at that time.
 
**`main.log`** — on every startup, for **all** servers (including the two that work):
 

[warn] UtilityProcess Check: Extension files not found in installed extensions
[warn] UtilityProcess Check: Extension obsidian not found in installed extensions
[warn] UtilityProcess Check: Extension obsidian-data not found in installed extensions

 
Since this warning also appears for the working servers, it is likely not the discriminating factor by itself, but it may be relevant to how `tools/call` routing decisions are made.

Steps to Reproduce

1. Windows, Claude Desktop MSIX build 1.24012.1.0.
2. npm install -g @modelcontextprotocol/server-filesystem (any version; 2026.1.14 and 2026.7.10 both reproduce).
3. claude_desktop_config.json:

{
  "mcpServers": {
    "metisfs": {
      "command": "C:\\Program Files\\nodejs\\node.exe",
      "args": [
        "C:\\Users\\USER\\AppData\\Roaming\\npm\\node_modules\\@modelcontextprotocol\\server-filesystem\\dist\\index.js",
        "C:\\Users\\USER\\SOME_DIRECTORY"
      ]
    }
  }
}

1. Restart Claude Desktop completely. Confirm handshake success in mcp-server-files.log (initialize → tools/list OK; tools are visible to the model).
2. In any chat (new or existing), ask Claude to list the allowed directories or list files.
3. Observe: instant Failed to call tool in the UI; no tools/call entry ever appears in the server log.

Claude Model

Other

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Claude Desktop build prior to the 2026-07-20~22 auto-update (exact version unknown; current broken build is MSIX 1.24012.1.0). Server-side: @modelcontextprotocol/server-filesystem 2026.1.14 worked on 2026-07-18.

Claude Code Version

Not applicable — this is a Claude Desktop bug (app 1.24012.1.0)

Platform

Other

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

• The failure is selective: two HTTP-remote MCP servers work in the same sessions while the filesystem server fails under every launch method including the identical HTTP-remote transport (test 7). This suggests the routing decision that drops tools/call is made per-server based on something other than transport, name, or server version — possibly interaction with the app's newer built-in file-access features (Cowork), e.g. tool-name or capability-level interception.
• Happy to provide full logs (main.log, mcp-server-files.log, supergateway console output) on request.