[BUG] Dynamic tools are registered but cannot be used

Environment

• Platform (select one):
• [ ] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [*] Other: Claude Desktop Claude 0.11.6 (0aa9ce) 2025-06-29T21:59:05.000Z
• Operating System: MacOS Sequoia, Version 15.5

Bug Description

I have a local proxy, that inside connect to other remote MCP server and registers its resources, prompts and tools ad dynamic resources, prompts and tools on the proxy (with name scoping) after calling specific tool. The resources and tools dynamically registered do appear in the list of the resources and tools (as Claude Deskto reports) but they cannot be used.

According to Claude Desktop: available_tools: ["undefunedcom__send_message"]
But when trying to call it: Tool 'undefunedcom__send_message' not found.

Steps to Reproduce

1. Use the dxt, then instruct Claude Desktop to connect to website with the proxy tool connect_to_website with parameter https://undefuned.com
2. The website should be connected. After connection the Claude Desktop should get resources, prompts and tools update, as tynamic tools are registered.
3. One of the tool should be undefunedcom__send_message. Ask Claude to send a message to it and I see Tool 'undefunedcom__send_message' not found.

Expected Behavior

Expected is that the tool exists, is callable and returns Success status with information.

Actual Behavior

Ask Claude to send a message to it and I see Tool 'undefunedcom__send_message' not found.

Additional Context

I tested with MCP inspector and it works correctly (direct remote MCP server) and via Inspector I tried to connect to local proxy and connect to the remote MCP and it worked, too. In Claude Desktop I tried using editing the config with local code directly - error persists with tools and resources after dynamic registration visible, but not possible to call them.
The same with .dxt extension.

2 days ago (Friday around 21:00 UTC) both worked ok. No changes on the MCP server or proxy.

I do not see any error in mcp.log, neither in the log of my proxy (I mean logs of Claude app).

Dynamic registration is essential to the principle of my use case.

I'm trying to attach the dxt file (not yet registered in your extension directory, not able to debug it due this error) but github do not allow dxt attachment. The file can be downloaded here (and description here)