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Every command has a nautical name and a standard alias. Use whichever you prefer.

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harbor dock

Alias: harbor add
Dock a new MCP server into the harbor. 
harbor dock --name <name> --command <command> [--args <args>...] [--env <KEY=VALUE>...]
FlagDescription
--nameUnique name for the server
--commandExecutable to run
--argsArguments to pass to the command (comma-separated for multiple)
--envEnvironment variables (supports vault:KEY references)
Example: 
harbor dock --name memory --command npx --args @modelcontextprotocol/server-memory

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harbor undock

Alias: harbor remove
Undock a server and cast it off. 
harbor undock --name <name>

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harbor fleet

Alias: harbor list
Review your fleet of docked servers. Shows each server’s name, command, status, and enabled state. 
harbor fleet

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harbor launch

Alias: harbor start
Launch a server out to sea (start the process). 
harbor launch --name <name>

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harbor manifest

Alias: harbor status
Read the harbor manifest — shows the current state of all servers and hosts. 
harbor manifest

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harbor signal

Alias: harbor sync
Signal connected hosts to update their charts. This merges your docked servers into each host’s config file. 
harbor signal [--host <host>]
FlagDescription
--hostSync only to a specific host (optional)

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harbor lighthouse

Alias: harbor gateway
Light the lighthouse — start the HTTP/SSE gateway to expose your MCP servers over the network. 
harbor lighthouse [--port <port>]
FlagDescription
--portPort to listen on (default: 3100)
See the gateway guide for endpoint details.

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harbor scout

Alias: harbor search
Scout the seas for new MCP servers on the official MCP Registry. 
harbor scout <query>

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harbor chest

Alias: harbor vault
Open the treasure chest — manage secrets stored in your OS keychain. 
harbor chest set <key> <value>
harbor chest get <key>
harbor chest delete <key>
harbor chest list
See the vault guide for more details.

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harbor scuttle

Alias: harbor uninstall
Scuttle the ship — uninstall Harbor from your system. Removes Harbor-managed server entries from host configs, the app, and the CLI binary. 
harbor scuttle [--purge] [--dry-run] [--yes]
FlagDescription
--purgeAlso remove ~/.harbor/ config directory and vault secrets
--dry-runPreview what would be removed without making changes
-y, --yesSkip the confirmation prompt
You can also uninstall via the install script: 
curl -fsSL https://harbormcp.ai/install.sh | sh -s -- --uninstall