[BUG] Claude Desktop drops MCP tool call silently — no request reaches server, no error surfaced (macOS)

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?

Product: Claude Desktop (macOS)
MCP server affected: anytype (@anyproto/anytype-mcp@1.2.9), but the underlying failure is host-side and likely affects any stdio MCP server.

A get_object tool call to the anytype MCP server never reached the server process. Claude's chat response reported the tool "did not respond," but no request was ever dispatched — this was confirmed by cross-referencing three log sources.

What Should Happen?

When a tool call cannot be dispatched to an MCP server (e.g., because the app is about to restart its MCP connections), Claude should either queue/retry the call or surface a clear error to the user and to the model — not silently proceed as if the tool had been called and failed. The current behavior produced a response claiming "the MCP server didn't respond," which is inaccurate and made root-causing this take significant manual log archaeology.

Error Messages/Logs

**1. `mcp-server-anytype.log`** — no trace of the failed call


2026-07-10T22:11:17.994Z [anytype] [info] Message from client: method="tools/call" id=5 params
2026-07-10T22:11:18.171Z [anytype] [info] Message from server: id=5 result(1 blocks)
2026-07-10T22:31:12.724Z [anytype] [info] Shutting down server...


Between `id=5`'s success and the shutdown, there is no `Message from client: method="tools/call"` entry — meaning the failed call was never received by the anytype MCP server, successfully or otherwise.

**2. `mcp.log`** — same gap confirmed across *every* configured server, not just anytype


2026-07-10T22:11:18.171Z [info] [anytype] Message from server: id=5 result(1 blocks)
2026-07-10T22:31:12.719Z [info] [omnifocus] Shutting down server...
2026-07-10T22:31:12.720Z [info] [omnifocus] Client transport closed
...
2026-07-10T22:31:12.724Z [info] [anytype] Shutting down server...
... (14 more servers, all within the same ~5ms window)


Zero `tools/call` entries from any server between 22:11:18 and 22:31:12 — a 20-minute window with no MCP client activity logged at all, followed by a synchronized full shutdown of all servers.

**3. `main.log`** — not yet checked for this window. The file's verbosity (duplicate log lines, full extension-manifest JSON dumps on every sync) made it impractical to reach the 2026-07-10 22:11–22:31 UTC range using `tail`-based reads within a 1MB response limit. This is the one piece of evidence still missing to explain *why* the app went quiet for 20 minutes before restarting all MCP connections (sleep/wake, manual quit, background throttling, or an internal watchdog restart are all still possible).

Steps to Reproduce

Steps to Reproduce

Not reliably reproducible on demand. Observed once during normal use:

1. Multiple anytype:API-get-object calls succeeded normally over ~30 minutes (21:39:36, 21:51:49, 22:11:17 UTC on 2026-07-10), each returning a result within ~0.2s.
2. A subsequent call to the same tool, made shortly after 22:11:18 UTC, produced no server-side record at all.
3. At 22:31:12 UTC, all 16 configured MCP servers (anytype, obsidian, notion, zotero, workflowy, omnifocus, raindrop, context7, moneywiz, netnewswire, kosshi, Control Chrome, Read/Send iMessages, Read/Write Apple Notes, Control your Mac, Brave AppleScript) shut down simultaneously with Shutting down server... / intentional shutdown at the same millisecond, indicating an app-level process restart rather than a per-server failure.

Claude Model

Claude Desktop

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Claude 1.20186.1 (df1d8a)

Platform

Claude Desktop

Operating System

macOS

Terminal/Shell

Other

Additional Information

• 16 MCP servers configured via claude_desktop_config.json (mix of npx-launched Node servers, one Python venv server, one Node script)
• Anytype MCP: @anyproto/anytype-mcp@1.2.9, connecting to Anytype's local API at http://127.0.0.1:31009