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Claude Desktop updated briefly for me to a version that is unreleased while I was using it today. I saw that Anthropic overhauled MCP integration and there was a way to turn on/off each individual tool from each MCP server. The UI was using a Switch component. This accidentally was updated along with the new web search feature but shortly after was removed.
So it seems we will soon have a solution from this on the client side at least for Claude.
Claude code and other solutions for coding agents may already have tools that provide the same functionality as https://github.com/JetBrains/mcp-server-plugin which may confuse LLM's.
One of possible solutions may be a configuration that only expose certain tools, configurable via mcp-server args e.g.
or
More context here.
JetBrains/mcp-server-plugin#18 (comment)
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