I do it
It depends on how you are building your web app.
If you have custom database tables - and thus creating custom manager pages (views) that work with these custom database tables, then Check out modx documentation. Plenty of example setups you can use SVN/GIT to share code.
Your custom components - like the kind you download as packages - are separate from the modx core. Lets say you are doing ecommerce and you had a custom database table handling the products. You would write your custom component outside of the modx directory (or inside, it doesn’t matter) and thus be able to share the custom component folder on git/whatever.
So I have a folder called trunk->products or just products with all of my custom code. This code is still using the awesome Modx framework so it’s easy to code - not just random php crap.
Check the docs, read it over, making an entire web app with modx is not only doable but fast. Though i do work with Django-python and RubyonRails as well.