Programmatically remove/add plugin and or repositories as post install

Hi,

I'm today developing a script to install LMS on a headless server and I would like to keep reference to the official repo of LMS while changing the plugin installed by default and adding new ones to avoid painful or unwanted configuration to basic user.
Is there a way to perform the trick via CLI, API call or by altering config file the good old way ?

Hope this is clear enough

Thank you by advance for your kind support

Vincent S