You can use plugman command to install/uninstall custom cordova plugins.
To install plugman
npm install -g plugman
Install plugin command syntax:
plugman <install|uninstall> --platform <ios|android|blackberry10|wp8> --project <directory> --plugin <name|url|path>
Example:
plugman install --platform ios --project platforms/ios/ --plugin plugins/cordova-plugin-test/
For more plugman options check this link