Refactor the Codebase

[hmc-cs-mdrissi]

The current organization of files/folders is a bit of a mess along with being not very style consistent. For this issue we'll need some discussion on how to organize things. Like one thing I'd like is all modules to live in their own file (or very similar modules can share a file) and then live in a folder like layers. This is a task for the summer as it isn't needed for this semester's project to be complete.