Sorry to hop on a bit late, it took me a little while to prepare what I was going to show you. If you want to look at an example of a custom coded but non-library structure, take a look here:
https://github.com/ToasterTechFRC/Toaster-Base-Bot
It is built off of the iterative model but it has a structure similar to command-based. It does require a bit more knowledge of Java than entry-level but it does show how a custom structure can be created manually to fit your needs. I've also documented it as best I can. Our 2016 code (we haven't pushed our CMP code) is also on GitHub, but it is much messier and has significantly less comments although it does show how our structure can function with autonomous modes.