Manage MCP servers with the CLI

MCP servers give an agent tools: a database, a search engine, an issue tracker. Manyfold keeps an agent’s servers in the config its framework reads and writes them onto the agent’s machine. Claude Code, Codex and Gemini CLI agents take MCP servers; select the agent with --agent-id or MF_AGENT_ID.

See what an agent has

mf mcp list --agent-id agt_xxx

Servers are grouped by the config they live in. Claude Code has two: user (~/.claude.json, the default) and project (the workspace’s .mcp.json); Codex has global (~/.codex/config.toml) and Gemini CLI user (~/.gemini/settings.json). The list shows the names of a server’s headers and environment variables but never their values, and whether the config has reached the machine.

Add a server

A server reached over HTTP takes its URL; one the agent runs as a command takes the command after --, as claude mcp add does:

mf mcp add sentry https://mcp.sentry.dev/mcp \
  --header 'Authorization: Bearer <token>' --agent-id agt_xxx
mf mcp add pg --agent-id agt_xxx --env DATABASE_URL=<url> \
  -- npx -y @modelcontextprotocol/server-postgres

Everything after -- belongs to the server’s command line, so mf’s own options go before it. --scope project puts a Claude Code server in the workspace’s .mcp.json instead. Remove one with mf mcp remove <name>.

Each change is written to the machine at once. A sandbox that is asleep, or a computer whose daemon is not connected, gets it when it next connects; mf mcp push writes it again on demand.

Install from the catalog or your library

mf mcp catalog list --q github
mf mcp catalog get github
mf mcp install github --env GITHUB_TOKEN=<token> --agent-id agt_xxx

install takes a server from your MCP library, or else from the platform’s catalog. Catalog entries often carry placeholder values: fill them in with --env or --header. --as gives the server another name on the agent.

Keep servers you reuse in your library:

mf mcp library create pg --env DATABASE_URL=<url> \
  -- npx -y @modelcontextprotocol/server-postgres
mf mcp library list
mf mcp library delete pg --yes

Deleting a library server leaves the copies installed on agents in place.

Servers added on the machine

Manyfold’s config replaces the servers in those files whenever it writes them. A server added on the machine itself, with claude mcp add or by editing .mcp.json, is lost at the next write unless you read it in first:

mf mcp pull --agent-id agt_xxx

See also

• Manage skills with the CLI
• CLI command reference