The goal is to write papers in a fast, reproducible, and efficient way. The goal is to also write really, really good papers that are styled in a high quality manner.
Except the README.md and main.tex, there should be no files in the root. They should be put into one of the other folders, wherever it makes sense.
The main.tex file should only be a resting ground for content. No content should be added here, and must only be imported. This allows reproducibility, and conversion to various formats easily.