[Bug] Claude Desktop: MCP Filesystem tools/call never reaches server after starting new conversation

[andresjsc]

Pre-submission Checklist

• I have checked that this question would not be more appropriate as an issue in a specific repository
• I have searched existing discussions and documentation for answers

Question Category

• Protocol Specification
• SDK Usage
• Server Implementation
• General Implementation
• Documentation
• Other

Your Question

Environment

• OS: Windows 11
• Claude Desktop App (native, NOT browser)
• MCP Filesystem server status: running
• Claude Pro account
• Configured directories: C:\Users\GUSA CAPITAL\Documents, C:\Users\GUSA CAPITAL\source\repos, C:\Users\GUSA CAPITAL\Documents\excel

What happened

The Filesystem MCP tools worked correctly two days ago. After starting a new conversation today, all tool calls fail with "Failed to call tool" error. The server shows as "running" in Settings > Developer. No configuration changes were made.

What the logs show

I checked %APPDATA%\Claude\Logs\mcp-server-Filesystem.log (3,331 lines, 1.2MB — months of working history).

Every new conversation today shows this exact pattern:

2026-07-22T15:21:24.733Z [Filesystem] [info] Server started and connected successfully
2026-07-22T15:21:24.894Z [Filesystem] [info] Message from client: method="initialize" id=0
2026-07-22T15:21:25.991Z [Filesystem] [info] Message from server: id=0 result
2026-07-22T15:21:30.399Z [Filesystem] [info] Message from client: method="notifications/initialized"
2026-07-22T15:21:30.405Z [Filesystem] [info] Message from client: method="tools/list" id=1
2026-07-22T15:21:30.411Z [Filesystem] [info] Message from server: id=1 result

There is NO tools/call entry anywhere. The server initializes correctly and lists tools, but when Claude attempts to execute a tool (list_directory, list_allowed_directories), the call never reaches the server.

Root cause hypothesis

The app successfully completes the MCP handshake and lists available tools, but tool call messages are not being forwarded to the MCP server when a new conversation starts. This is a routing bug in Claude Desktop.

Reproduction steps

1. Have a working Filesystem MCP server configured in Claude Desktop
2. Start a NEW conversation
3. Ask Claude to use any Filesystem tool
4. Result: "Failed to call tool" error — tool call never appears in mcp-server-Filesystem.log

What I already tried

• Full restart of Claude Desktop (confirmed no background processes)
• Single instance only (no multiple windows)
• Both backslash and forward-slash path formats
• Multiple new conversations — same result every time

This is a regression. The same setup worked in a previous conversation two days ago.