It's not implemented yet. However, you can look under ~/.activator/<version>/config.json
and directly remove the application there. If you want to remove all the applications either delete the file or set to {"applications":[]}
We haven't documented the config.json format, because we haven't locked on a stable config file there yet, hence why it's under a versioned directory.
I believe there's already a ticket for the feature: https://github.com/typesafehub/activator/issues/17