Here are two common methods to configure them permanently — both survive restarts and will always auto-load when Claude Code launches.

Method 1: Command Line (Recommended)

Run the following command in your project directory:

claude mcp add serena -- uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context ide-assistant --project $(pwd)

• Automatically updates ~/.claude/settings.json
• Adds the serena MCP server into the configuration
• Will auto-connect each time Claude Code starts

Method 2: Manual Configuration File Edit

1. Open ~/.claude/settings.json
2. Add a new MCP server block, for example:

{
  "mcpServers": {
    "fujisoft-code-agent": {
      "command": "cmd.exe",
      "args": ["/c", "code-agent", "server"]
    },
    "serena": {
      "command": "uvx",
      "args": [
        "--from", "git+https://github.com/oraios/serena",
        "serena", "start-mcp-server",
        "--context", "ide-assistant",
        "--project", "/your/project/path"
      ]
    }
  }
}

• You can add multiple MCP servers here
• Save the file and restart Claude Code → the servers will auto-connect

Verify Your Configuration

To check your current MCP servers:

cat ~/.claude/settings.json

Or inside Claude Code:

/status

This will display the list of configured MCP servers and their status.

✅ Conclusion

• Command Line Method → Quickest and easiest, auto-writes to config
• Manual File Edit → More flexible, can add multiple servers at once
• Result is the same → Both are persistent and survive restarts

⚡ Pro Tip:
On Windows, replace $(pwd) with %cd% when running the command.
Example:

claude mcp add serena -- uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context ide-assistant --project %cd%

👉 With this setup, you can extend Claude Code with custom MCP servers like Serena and streamline your coding workflow!

🔹 Additional Knowledge: Execution Status & Management

After Adding Serena with --project

• When you run: claude mcp add serena --project $(pwd)
  • Serena will only auto-start when you run Claude Code inside that project directory.
  • Other directories will not see Serena.

Manage and Modify MCP Servers

1. List configured MCP servers: claude mcp list
2. Remove Serena from config: claude mcp remove serena
3. Re-add as a global configuration (visible everywhere): claude mcp add serena -- uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context ide-assistant
4. Add Serena to another project (project-level): cd /path/to/other/project claude mcp add serena -- uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context ide-assistant --project $(pwd)

Config File Locations

• Project-level config → created inside the project directory
• Global config → stored in ~/.claude/settings.json

If you want to switch Serena from project-level to global:

1. Remove the existing entry claude mcp remove serena
2. Add it again without --project.