GitHub Copilot CLI

Copilot CLI reads the Foundry Connect plugin repository as a marketplace and installs the same plugin Claude Code uses. One install gives you the foundry-pipelines skill, the three /foundry-* commands, and the foundry MCP connection.

New here? Do Getting Started first.

Measured against GitHub Copilot CLI 1.0.83.

Step 1 — install the plugin

Run these at the Copilot prompt:

copilot plugin marketplace add UMMS-Biocore/foundry-connect-plugin
copilot plugin install foundry-connect@foundry-connect

Step 2 — point it at your instance

Copilot has no per-plugin settings dialog, so you supply your instance as an environment variable. Set instance_host to your hostname only:

export instance_host=foundry.your-org.edu

No https://, no trailing slash, and no /mcp. The plugin builds https://<instance_host>/mcp itself, and adding any of those pieces yourself produces an address that cannot connect.

Put that export in your shell profile. A new terminal without the variable set cannot reach your instance, and the failure is quiet rather than loud.

Step 3 — restart Copilot

MCP servers are read once, when a session starts. The plugin you just installed is not connected until you start a new session.

Step 4 — check it worked

copilot mcp list

You should see:

Plugin servers:
  foundry (http)

For the fuller picture, copilot plugins list (plural) is the real inspector: it shows plugins, MCP servers and skills together with their scope.

Signing in

The plugin's connection carries no token, so it uses OAuth. Copilot handles this properly: when Foundry Connect refuses an unauthenticated request, Copilot reads the sign-in address out of that response and follows it. Approve access once and you are connected.

Copilot CLI has no copilot mcp login command, so sign-in happens inside an interactive session rather than as a separate step you run first. If you would rather not use OAuth, supply a Personal Access Token as a header instead; Copilot expands environment variables inside header values, so the token does not have to sit in the file as literal text.

Troubleshooting

Symptom	Cause	Fix
No `Plugin servers` section in `copilot mcp list`	The address was rejected, and Copilot drops an invalid entry silently	Check `instance_host` is set, and is a bare hostname
Server listed but never connects	Session started before the variable was set	Set the variable, then start a new session
Tools missing after install	MCP config is read at session start	Start a new session

The silence is the thing to watch for. An invalid entry in ~/.copilot/mcp-config.json is dropped with no error printed anywhere, so a missing server is far more likely than a broken one.