Themes & MU-plugins: Nested repositories, GIT Submodules or something entirely different?

Yes, a sub-domain install with domain mapping, and multiple sites.

I have a bunch of custom plugins (and mu-plugins) as well as themes, that I’d like to manage independently of the main project (on bedrock). Locally I’ve set these up in their own directories, outside of the project, and pushed them up to bitbucket.

I’m trying to use composer as you suggested but having some problems that I noted over here:

http://discourse.roots.io/t/best-way-to-install-private-paid-plugins-with-composer/1045/8