Command Reference

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

harbor dock

Alias: harbor add

Dock a new MCP server into the harbor. Supports three modes: native (one-click catalog), custom stdio, and custom remote.

Native servers

Dock a server from Harbor’s built-in catalog with a single command:

harbor dock <native-id> [--name <name>] [--skip-auth] [--disabled] [--auto-start] [-- <extra-args>...]

Flag	Description
`<native-id>`	Server id from the catalog (e.g., `github`, `slack`, `filesystem`)
`--name`	Override the default server name
`--skip-auth`	Dock now, authorize later
`--disabled`	Keep moored (disabled) initially
`--auto-start`	Start automatically when Harbor launches
`-- <args>`	Extra arguments appended after the catalog defaults

Examples:

# Dock GitHub (remote, needs a PAT in the vault)
harbor dock github

# Dock filesystem with allowed directories
harbor dock filesystem -- ~/Documents ~/Projects

# Dock Slack (opens browser for OAuth)
harbor dock slack

# Dock with a custom name
harbor dock atlassian --name my-jira

See the native servers guide for the full catalog.

Custom stdio servers

harbor dock --name <name> --command <command> [--args <args>...] [--env <KEY=VALUE>...]

Flag	Description
`--name`	Unique name for the server
`--command`	Executable to run (e.g., `npx`, `node`, `python`)
`--args`	Arguments to pass (comma-separated for multiple)
`--env`	Environment variables (supports `vault:KEY` references)
`--auto-start`	Start automatically when Harbor launches
`--disabled`	Keep moored (disabled) initially

Example:

harbor dock --name memory --command npx --args "-y,@modelcontextprotocol/server-memory"

Custom remote (HTTP) servers

harbor dock --name <name> --url <url> [-H <KEY:VALUE>...] [--env <KEY=VALUE>...]

Flag	Description
`--name`	Unique name for the server
`--url`	URL of the remote MCP HTTP endpoint
`-H`, `--header`	Custom HTTP headers (`KEY:VALUE`, can be repeated)
`--env`	Environment variables (supports `vault:KEY` references)

Example:

harbor dock --name my-api --url https://mcp.example.com/v1/mcp \
  -H "Authorization:Bearer vault:my_api_key"

harbor undock

Alias: harbor remove

Undock a server and cast it off.

harbor undock --name <name>

harbor fleet

Alias: harbor list

Review your fleet of docked servers. Shows each server’s name, command/url, status, and enabled state.

harbor fleet [--host <host>]

Flag	Description
`--host`	Filter servers bound to a specific host (optional)

harbor launch

Alias: harbor start

Launch a server out to sea (start the process).

harbor launch --name <name>

harbor manifest

Alias: harbor status

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

harbor manifest

harbor signal

Alias: harbor sync

Signal connected hosts to update their charts. This merges your docked servers into each host’s config file.

Syncing happens automatically when you dock, undock, toggle, or connect a host. You only need harbor signal to force a manual re-sync.

harbor signal [--host <host>]

Flag	Description
`--host`	Sync only to a specific host (optional)

harbor port

Alias: harbor host

Manage host connections. Users opt in to each host individually.

harbor port                    # List all hosts with link status
harbor port link <host>        # Link a host to start syncing
harbor port unlink <host>      # Unlink a host

Valid hosts: claude, claude-desktop, codex, vscode, cursor

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>] [--host <host>] [--expose] [--token <token>]

Flag	Description
`--port`	Port to listen on (default: `3100`)
`--host`	IP to bind to (default: `127.0.0.1`)
`--expose`	Shorthand for `--host 0.0.0.0` (expose to network)
`--token`	Bearer token required for remote (non-localhost) access

See the gateway guide for endpoint details.

harbor publish

Alias: harbor broadcast

Broadcast your gateway to the high seas — publish your local MCP tools to the internet via a secure QUIC tunnel.

harbor publish [--relay <addr>] [--subdomain <name>] [--relay-key <hex>] [--transport <type>] [--port <port>] [--tools <tool,...>]

Flag	Default	Description
`--relay`	`relay.harbormcp.ai`	Relay server address (hostname or `host:port`)
`--subdomain`	auto-assigned	Requested subdomain (e.g. `myname` → `myname.relay.harbormcp.ai`)
`--relay-key`	auto-fetched	Relay’s public key (hex) — required for self-hosted relays
`--transport`	`quic`	Transport to use: `quic` (default) or `cloudflare`
`--port`	from config	Local gateway port to tunnel (default: `3100`)
`--tools`	all	Comma-separated tool allowlist for remote access

Examples:

# Zero-config publish via managed relay
harbor publish

# Custom subdomain
harbor publish --subdomain myname

# Self-hosted relay
harbor publish --relay relay.example.com:7800 --relay-key <hex-key>

# Cloudflare Tunnel (requires cloudflared installed)
harbor publish --transport cloudflare

# Expose only specific tools remotely
harbor publish --tools get_issues,search_code

See the publishing guide for full details.

harbor relay

Run a self-hosted Harbor relay server.

harbor relay [--quic-port <port>] [--https-port <port>] [--domain <domain>] [--keypair-file <path>] [--print-key]

Flag	Default	Description
`--quic-port`	`7800`	Port for QUIC tunnel listener (UDP)
`--https-port`	`8443`	Port for HTTPS frontend (TCP)
`--domain`	`relay.harbormcp.ai`	Domain for subdomain routing
`--keypair-file`	`/data/harbor-relay/keypair`	Path to persist the relay keypair
`--print-key`	—	Print the relay’s public key and exit
`--auth-token`	—	Require this token from all tunnel clients

Examples:

# Start relay with default settings
harbor relay --domain relay.example.com

# Print the relay's public key (share with tunnel clients)
harbor relay --print-key --keypair-file /data/harbor-relay/keypair

See the self-hosting guide for deployment instructions.

harbor cargo

Alias: harbor filter

Manage tool filtering — control which tools each server exposes.

harbor cargo allowlist <server> [tools...]   # Set tool allowlist
harbor cargo blocklist <server> [tools...]   # Set tool blocklist

harbor scout

Alias: harbor search

Scout the seas for new MCP servers on the official MCP Registry.

harbor scout <query>

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.

harbor crew

Alias: harbor team

Share MCP server configs across your team via a git-backed fleet repository. Secrets stay local — only vault:KEY_NAME references are committed. See the team sync guide for a full walkthrough.

harbor crew init

Initialize ~/.harbor/fleet/ as a git repository. Optionally links a remote so teammates can clone the same fleet.

harbor crew init [--git <url>]

Flag	Description
`--git`	Git remote URL (SSH or HTTPS) to push/pull the fleet config

Examples:

# Local-only fleet (add a remote later)
harbor crew init

# Initialize and link a remote in one step
harbor crew init --git [email protected]:your-org/fleet.git

harbor crew join

Join an existing team fleet by cloning its git repository and auto-merging its servers into your local config.

harbor crew join <git-url>

harbor crew push

Push local fleet-managed servers to the shared repository. Pass server names to mark local servers as fleet-managed before pushing.

harbor crew push [<servers>...] [--message <msg>]

Flag	Description
`<servers>`	Names of local servers to mark as fleet-managed and include
`-m`, `--message`	Commit message (default: `"Update fleet config"`)

Examples:

# Share two existing servers with the team
harbor crew push github linear

# Push with a custom commit message
harbor crew push -m "Add Slack server"

harbor crew pull

Fetch upstream changes and 3-way merge fleet servers into your local config.

harbor crew pull [--dry-run]

Flag	Description
`--dry-run`	Preview what would change without applying anything

Servers you have edited locally since the last pull will be skipped (locally modified). Harbor never silently overwrites your changes. To accept the upstream version, run harbor undock <name> then harbor crew pull. To share your version instead, run harbor crew push <name>.

harbor crew status

Show local vs fleet drift — git sync status (ahead/behind) and per-server state.

harbor crew status

harbor crew provision

Prompt for vault secrets required by fleet servers that aren’t yet stowed locally.

harbor crew provision [--dry-run]

Flag	Description
`--dry-run`	Show missing keys without prompting for values

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]

Flag	Description
`--purge`	Also remove `~/.harbor/` config directory and vault secrets
`--dry-run`	Preview what would be removed without making changes
`-y`, `--yes`	Skip the confirmation prompt

You can also uninstall via the install script:

macOS / Linux
Windows

curl -fsSL https://harbormcp.ai/install.sh | sh -s -- --uninstall

$env:HARBOR_UNINSTALL=1; irm https://harbormcp.ai/install.ps1 | iex

harbor update

Update Harbor to the latest version. Checks GitHub releases, downloads the appropriate binary for your platform, verifies the SHA256 checksum, and replaces the current binary.

harbor update

Flags

Flag	Description
`--check`	Just check for updates without installing
`-y, --yes`	Skip the confirmation prompt

Examples

# Check if an update is available
harbor update --check

# Update without confirmation
harbor update --yes

Harbor also checks for updates automatically in the background. If a newer version is available, a notice appears after any command (checked once every 24 hours).

Get Started

Desktop App

CLI

Guides

Configuration

Development

Command Reference

harbor dock

Native servers

Custom stdio servers

Custom remote (HTTP) servers

harbor undock

harbor fleet

harbor launch

harbor manifest

harbor signal

harbor port

harbor lighthouse

harbor publish

harbor relay

harbor cargo

harbor scout

harbor chest

harbor crew

harbor crew init

harbor crew join

harbor crew push

harbor crew pull

harbor crew status

harbor crew provision

harbor scuttle

harbor update

Flags

Examples

Get Started

Desktop App

CLI

Guides

Configuration

Development

Documentation Index

​harbor dock

​Native servers

​Custom stdio servers

​Custom remote (HTTP) servers

​harbor undock

​harbor fleet

​harbor launch

​harbor manifest

​harbor signal

​harbor port

​harbor lighthouse

​harbor publish

​harbor relay

​harbor cargo

​harbor scout

​harbor chest

​harbor crew

​harbor crew init

​harbor crew join

​harbor crew push

​harbor crew pull

​harbor crew status

​harbor crew provision

​harbor scuttle

​harbor update

​Flags

​Examples

harbor dock

Native servers

Custom stdio servers

Custom remote (HTTP) servers

harbor undock

harbor fleet

harbor launch

harbor manifest

harbor signal

harbor port

harbor lighthouse

harbor publish

harbor relay

harbor cargo

harbor scout

harbor chest

harbor crew

harbor crew init

harbor crew join

harbor crew push

harbor crew pull

harbor crew status

harbor crew provision

harbor scuttle

harbor update

Flags

Examples