MCP tool calls never reach Filesystem-type servers after Desktop update — server healthy, tools/call never sent by client

### What happened?

Following a Claude Desktop update, every tool call to Filesystem-type MCP servers fails with a generic client-side error ("Tool execution failed"), while Desktop's Local MCP servers settings panel shows the server as "running" (blue/healthy status) — no red/failed indicator. Server-side logs confirm the server itself starts cleanly and completes the initialize → tools/list handshake successfully every time, but no tools/call entry ever appears in the server log corresponding to any attempted tool call. The request is never reaching the server process — the regression is in Desktop's client-side MCP routing after the handshake, not in the server implementation.

### What did you expect to happen?

Tool calls (e.g. list_allowed_directories, list_directory) should be sent to the MCP server and return results, as they did prior to the update.

### Steps to reproduce

1. Update Claude Desktop (macOS)
2. Configure or use an existing Filesystem-type MCP server
3. Attempt any tool call (e.g. list_allowed_directories)
4. Observe: call fails immediately with a toast notification naming the specific tool, e.g. Failed to call tool "list_allowed_directories". — despite the server showing "running" status in Local MCP servers settings. Same pattern for every tool attempted (list_directory, etc.), each producing its own tool-specific failure toast.

### Area

Tool Discovery / Invocation

### MCP Server (if applicable)

Filesystem — reproduced on both Anthropic's bundled Filesystem extension AND a separately-configured server (different name) running a fresh npm install of @modelcontextprotocol/server-filesystem

### Error messages or logs

```shell
Client-side: Failed to call tool "[tool_name]". toast per attempted call.
Server-side (View Logs, Filesystem server) — clean handshake, no errors:

[Filesystem] [info] Server started and connected successfully
[Filesystem] [info] Message from client: method="initialize" id=0
[Filesystem] [info] Message from server: id=0 result
[Filesystem] [info] Message from client: method="notifications/initialized"
[Filesystem] [info] Message from client: method="tools/list" id=1
[Filesystem] [info] Message from server: id=1 result

No tools/call entry ever appears afterward, despite multiple tool call attempts made in that session.
```

### Additional context

Ruled out: stale server registration, naming collision with the bundled extension, config/path issues, server-side crash. All other MCP servers on the same Desktop instance (LibreOffice/UNO bridge, GnuCash, ProtonMail, two Gmail server instances) continued routing and responding normally throughout, isolating this to Filesystem-type servers. Bundled extension reports @modelcontextprotocol/server-filesystem v2026.7.4 underneath the hood. A second Desktop update pushed later the same day did not resolve the issue — retested and reproduced identically afterward.