How to filter which JetBrains MCP tools are exposed to Claude Code?

Question

I use the JetBrains MCP server (@jetbrains/mcp-proxy) with Claude Code, and the IDE tools it exposes overlap with Claude Code's built-in tools and confuse the LLM. Is there a way to enable or disable specific tools in the mcpServers configuration? I saw --enabled_tools / --disabled_tools flags proposed in the issue, but I couldn't tell whether they are actually supported.

Originally asked on GitHub: https://github.com/JetBrains/mcp-jetbrains/issues/34

AgentArmor team · Accepted Answer

Status: open. This issue is a feature request for filtering JetBrains MCP tools, and the thread does not report a working built-in flag.

The issue proposes adding filter flags to the server arguments in an mcpServers configuration, for example:

```json
{
  "mcpServers": {
    "jetbrains": {
      "command": "npx",
      "args": ["-y", "@jetbrains/mcp-proxy", "--enabled_tools", "mcp__jetbrains__get_open_in_editor_file_text"]
    }
  }
}
```

or using `--disabled_tools` with the same tool name. This is a proposal in the issue, not a confirmed implementation, so the thread gives no evidence that these flags work on a released version of the proxy.

One commenter shared a temporary workaround: a separate tool-filtering proxy at https://github.com/Lewik/mcp-tools-proxy, saying they hoped tool filtering would become a default client feature. The comment does not include setup instructions, so check that project for usage details.

Another commenter reported that an unreleased Claude Desktop build briefly showed per-tool on/off switches for each MCP server, suggesting Anthropic is moving toward client-side filtering, but that build was removed shortly after. The thread does not mention any similar client-side filtering in Claude Code.

AgentArmor team · Answer

**What a GitHub user tried on GitHub** (Outcome unclear)

Proposed passing --enabled_tools or --disabled_tools with a JetBrains tool name in the @jetbrains/mcp-proxy args inside an mcpServers configuration. This was presented as a possible solution, not as something already tested.

Source: https://github.com/JetBrains/mcp-jetbrains/issues/34

AgentArmor team · Answer

**What @Lewik tried on GitHub** (Outcome unclear)

Suggested using the third-party Lewik/mcp-tools-proxy as a temporary solution for filtering MCP tools. No setup details were given in the thread.

Source: https://github.com/JetBrains/mcp-jetbrains/issues/34#issuecomment-2797322906

AgentArmor team · Answer

**What @jpicklyk tried on GitHub** (Outcome unclear)

Reported seeing per-tool enable/disable switches for MCP servers in a briefly installed, unreleased Claude Desktop build, which was removed shortly after.

Source: https://github.com/JetBrains/mcp-jetbrains/issues/34#issuecomment-2846075280

How to filter which JetBrains MCP tools are exposed to Claude Code?

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How to filter which JetBrains MCP tools are exposed to Claude Code?

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