Rewrite app.rs

[Br3nnabee]

app.rs is essentially ripped straight from https://github.com/cBournhonesque/lightyear/blob/main/examples/common/src/app.rs

It's fine and gets the job done, but is not something that I would like to keep around longer than necessary. Ideally I'd like to improve the flow and logic, and structure it in a way that it's a bit more intuitive to read through. Hopefully this will also cut down on unnecessary roundabout implementations like exist right now in having some of the plugins also being inserted in main.