Re-structure code source

[igniscyan]

For the sake of keeping the project easy to work with/contribute to, I think it's worth restructuring how we're keeping source files for now. A good example we can try and follow is located at this link

If I get approval to work on this, I'll look into getting Docker to work with the new layout as well.

[mirdaki]

I haven't thoroughly looked through it yet, but it seems to be a good example (though a little more complex than we might need).

I wanted to add we should switch to using more dependency injection, at least with the models to use the database connection. This makes the architecture a little more clean and much more testable (tests fail now because there is no database to connect to).