Every time I get involved in a project it seems to start with this neatly organised tree where everything is squirreled away.
By contrast my own systems are often just one giant folder. Conceptually I'm just not bothered by large directories with 20000 files. And I'm happy to mix files of different types in one folder (OMG .c files and .ico files in the same folder like a barbarian!!!)
I find the system is simple, and everything I need is in one place. But it freaks people out.
I guess we're all just wired differently.
(Obviously there is organisation, I have different projects in different folders etc, but there's no "extra" organisation. I don't make more folders just because this one is "full".)