@Brophy What I do with my custom plugin is
git clone nodebb-plugin-my-plugin into the server user's home folder,
then in the nodebb's root folder:
npm link nodebb-plugin-my-plugin. And I never lose the plugin, if I have to release a new update I just do a
git pull in the plugin (original) folder, then is updated automatically when I restart the forum.
So in your case I'd say create the
nodebb-theme-your-theme folder somewhere in your server, do
npm link and then in nodebb
npm link nodebb-theme-your-theme .
But I think this is suggested for development environments, not for production, even if in my case is working pretty well
Another way to do it is to install your theme with
npm install git+https://firstname.lastname@example.org/<your-git-user>/<your-private-theme-repo>.git