At the time I was new to provisioning a web server from scratch and ended up doing a lot of things just to get to a working state. Over time it's evolved as I learnt new tricks, leaving a mess in the process.
This seems to be a problem with any project in both the cyber and physical world. As you create more of something, you need to decide where to put them and reorganise everything else. Making it refactoring essentially.
Anyway, for this article I'm strictly talking about directory structures and where to put files used by a web server. No matter which web server you're using, the solution probably applies equally.