Claude Code integration¶

MESA registers each server as a local stdio MCP server: Claude Code launches the binary as a subprocess and talks to it over standard input/output. No network ports, no hosted service required. Claude Code is one of four clients MESA supports — see also Codex CLI, Antigravity, and OpenCode.

Scopes¶

The installer uses user scope (-s user) so the servers are available in every Claude Code project on your machine. The three scopes Claude Code supports:

Scope	Stored in	Visible to
`local`	your user config, keyed to the current project	just you, just this project
`user`	your user config	you, every project (MESA default)
`project`	`.mcp.json` committed in the repo	everyone who clones the repo

Override with MCP_SCOPE, e.g. MCP_SCOPE=project to drop a shareable .mcp.json into the current directory instead.

Managing the servers¶

claude mcp list                 # show all servers + health
claude mcp get mesa-mcp         # show one server's config
claude mcp remove mesa-mcp -s user

The registration MESA creates¶

User-scope registrations live in ~/.claude.json; project scope lands in a .mcp.json committed at the repo root.

{
  "mcpServers": {
    "mesa-mcp":  { "type": "stdio", "command": "~/.mesa/.venv/bin/mesa-mcp",
                   "args": ["--transport", "stdio"], "env": {} },
    "irods":     { "type": "stdio", "command": "~/.mesa/bin/irods-mcp-server",
                   "args": ["-c", "~/.mesa/repos/irods-mcp-server/config-stdio.yaml"], "env": {} },
    "formation": { "type": "stdio", "command": "~/.mesa/bin/formation-mcp",
                   "args": ["--transport", "stdio"], "env": {} }
  }
}

mesa-ducklake is not listed here

mesa-ducklake is a library imported by mesa-mcp, not a separate MCP server. Its capabilities surface through mesa-mcp's mesa_ducklake_* tools. See its page.

Conflicting scopes¶

If claude mcp list warns that a server is "defined in multiple scopes", you have the same name registered more than once (e.g. an older hand-rolled entry plus the MESA one). Keep the one you want and remove the rest:

claude mcp remove mesa-mcp -s user
claude mcp remove mesa-mcp -s local

Alternative: hosted / remote servers¶

Local stdio is the default and needs no auth for public data. CyVerse also runs hosted MCP endpoints you can connect to instead of building locally — for example the public iRODS server at https://mcp.cyverse.ai/mcp:

claude mcp add --transport http cyverse-irods https://mcp.cyverse.ai/mcp

Hosted mesa-mcp (Streamable HTTP / SSE behind CyVerse Keycloak OIDC) is documented in the mesa-mcp repo; it requires authentication. The MESA installer focuses on the local build because it works offline-of-auth and gives you live, editable source.