[FEATURE] Documentation/support for Claude Code

[manymorph]

Feature Description

Documentation and/or tooling to help users register the MCP server with Claude Code (Anthropic's CLI tool), which uses a separate configuration system from Claude Desktop.

Use Case & Motivation

Claude Code is becoming widely used for development workflows. Users who work with Obsidian vaults as knowledge bases benefit greatly from the search tools (semantic search, Dataview queries), even when they have direct filesystem access through Claude Code.

Currently, the plugin registers smoothly with Claude Desktop, but Claude Code uses a completely separate MCP configuration system (on Windows: ~/.claude.json rather than %APPDATA%\Claude\claude_desktop_config.json). Users have to figure out the setup process through trial and error.

Proposed Solution

The simplest solution is to add a "Claude Code Setup" section to the README. Obviously, if this could be automated that's even better. To get this started, I believe these are the steps I went through (with Claude Code's help) to get the server registered to my Claude code:

1. Add the server via CLI
claude mcp add --transport stdio obsidian-mcp-tools --scope user -- "C:\path\to\mcp-server.exe"

This creates an entry in ~/.claude.json (on Windows: C:\Users<username>.claude.json)

2. Manually add environment variables
The CLI command creates the server entry but with an empty env: {} object. Manually edit ~/.claude.json to
add the API key:

  "mcpServers": {
    "obsidian-mcp-tools": {
      "type": "stdio",
      "command": "C:\\path\\to\\mcp-server.exe",
      "args": [],
      "env": {
        "OBSIDIAN_API_KEY": "your-api-key-here"
      }
    }
  }

[chipshadd]

For Claude Code running in WSL I ran into issues where the windows MCP executable was not seeing the api key being passed in via env: {}.
The following config is what ended up working for me:

"mcpServers": {
  "obsidian-mcp-tools": {
      "type": "stdio",
      "command": "cmd.exe",
      "args": [
        "/c",
        "set OBSIDIAN_API_KEY=<api-key> && C:\\path\\to\\vault\\.obsidian\\plugins\\mcp-tools\\bin\\mcp-server.exe"
      ]
    }
  }