Customizing and maintaining themes/plugins
So, I'm off and running with our new site, and most everything is how I want it. For the moment. Long term though, not as much. For instance, I hate using a plugin like CSSEdit to customize CSS, and Pocket to insert JS to manipulate my theme's layout (using the Bootstrap theme). I'm a big Wordpress guy, and I'm used to the idea of things like child themes and such to modify without altering a parent layout. From what I can tell, no such thing exists for Vanilla though.
This isn't so much a question, I'm mostly just curious how others handle their customizations. Ideally, I want to not mess with other people's code as much as possible. But I also don't like purely forking a resource, since then you have to backport any future updates they make. The same obviously goes for plugins that don't do things quite the way I want.
I'm gonna put this all in a git repo. That's happening no matter what. I'm just wondering what best practices you find work really well for Vanilla. I'm saying all this while still reviewing the dev docs and such, trying to learn the system.