Yes that’s it exactly - through the docker/production install, you shouldn’t need to do any sort of filesystem maintenance, as it is a config for any plugin installs in your app.yml. Under the hood, plugins are cloned into the plugins directory on build.
In a dev env where you want to have control and build, develop, or alter your environment, use symlinks.
(Hi by the way, I think I recall that we ran into each other on University a little while ago 
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