[BUG] Claude Desktop loads partial MCP tool set from Craft MCP server; Cowork loads full set from same endpoint

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?

Hi, I'm reporting a bug with Claude Desktop (Chat, not Claude Code) where MCP tools from a connected Craft MCP server load incompletely.

The problem:
Claude Desktop consistently loads only a subset of tools from my Craft MCP server. Key write tools (blocks_add, blocks_update, blocks_delete, markdown_add) are missing from the session. The same MCP endpoint URL, with the same read-and-write permissions, loads the full tool set when connected through Cowork.

This has persisted across at least 3 separate sessions. Between sessions I have:

• Disconnected and reconnected the Craft MCP integration
• Fully quit and restarted Claude Desktop
• Confirmed in Craft's settings that the MCP connection is set to read and write

None of these steps resolved the issue.

What loads in Claude Desktop (partial list):
blocks_get, blocks_move, collectionItems_add, collectionItems_update, collectionItems_delete, collectionSchema_get, comments_add, documents_create, whiteboard tools

What's missing in Claude Desktop but works in Cowork:
blocks_add, blocks_update, blocks_delete, markdown_add, documents_delete, documents_list, documents_search, document_search, folders_, tasks_, collections_list, collections_create, collectionSchema_update

Cowork confirmation:
I opened a Cowork session with the same Craft MCP endpoint and asked Claude to verify its tools. It confirmed the full tool set was loaded. I then had it run a complete write test: create a doc, add markdown, update a block, and delete the doc. All four operations succeeded. The MCP server is serving all tools correctly.

This points to Claude Desktop specifically failing to load the full tool manifest from the MCP server.

Environment:

• macOS Tahoe 26.1 (Claude Desktop app)
• Craft MCP server (mcp.craft.do endpoint)
• Plan: Pro Max
• Claude Desktop version: Claude 1.3109.0 (35cbf6) 2026-04-16T20:32:01.000Z

This is blocking my workflow. I use Craft MCP extensively for knowledge management and the missing write tools mean I can't update existing documents from Claude Desktop sessions.

What Should Happen?

Claude Desktop should load the complete set of MCP tools from the Craft MCP server, identical to what Cowork loads from the same endpoint. Specifically, blocks_add, blocks_update, blocks_delete, markdown_add, documents_delete, documents_list, documents_search, document_search, folders_, tasks_, collections_list, and collectionSchema_update should all be available. These tools are confirmed working when the same MCP URL is connected through Cowork.

Error Messages/Logs

No error messages are shown in the UI. The missing tools simply don't appear in the session. Claude Desktop does not surface any warning that tools failed to load.
Console.app on macOS shows no results when filtering by "Claude", "claude", "Electron", or "MCP". No log files found at ~/Library/Logs/Claude/. Happy to provide logs if given guidance on the correct process name or log file location for Claude Desktop.

Steps to Reproduce

1. Connect Craft MCP server to Claude Desktop using a /links/ endpoint URL (e.g. [https://mcp.craft.do/links/[id]/mcp](https://mcp.craft.do/links/%5Bid%5D/mcp)) with read and write permissions confirmed in Craft's Imagine settings
2. Start a new chat in Claude Desktop
3. Ask Claude to list its available Craft tools or attempt to use blocks_add, blocks_update, or markdown_add
4. Observe that these tools are missing. Only a subset loads (blocks_get, blocks_move, collectionItems_add/update/delete, collectionSchema_get, comments_add, documents_create, whiteboard tools)
5. Open Cowork with the same Craft MCP endpoint
6. Ask Claude to list its available Craft tools
7. Observe that the full tool set loads, including blocks_add, blocks_update, blocks_delete, markdown_add, documents_delete, documents_list, documents_search, folders_, tasks_
8. In Cowork, run a write test (create doc, add markdown, update a block, delete doc). All succeed, confirming the MCP server is serving full read-write capabilities

This has reproduced across 3+ separate Claude Desktop sessions. Between sessions I have disconnected and reconnected the Craft MCP integration, fully quit and restarted Claude Desktop, and confirmed read-write permissions in Craft. None of these steps resolved the issue.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.68 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_