That means the core project cannot list its plugins as dependencies. You will instead want to be able to load plugins from a configuration file.
(The problem is actually equally awkward in languages that have package systems, such as Node and Ruby. In Ruby, for example, a program can only see gems declared in the Gemfile; same problem with npm-shrinkwrap.json.)
I suppose you could set up a special build system where plugins are expected to be installed into a certain folder so that they're statically built in, with some kind of hook so that they're registered into the core. That's the Nginx approach. I'm not a big fan, especially since this method of building things need to be reinvented for each app that needs a plugin system.
You could, of course, invert the relationship and make this system a library: To set it up with your plugins, you write a small program that runs the system's main entrypoint with a list of plugins. But that just makes it harder to configure, build, use and deploy.