Paul Graham On 'Great Hackers'
You're using many of the same languages as I am.
I would say that if your team is using IntelliJ, and you're using emacs, you should not blame everyone else for the confusing directory structure. Teams should use the same tools. One of my descriptions for a software engineer is that they work very closely with their team. Some methodologies even call for pair programming. Hard to do when you can't even agree on an editor.
My second point is, I've never used an IDE that forced, or even recommended, a particular directory structure. I use VS6, VS.NET, and Eclipse primarily, and I have complete control over the directory structure. There are probably reasons why your project had that particular directory structure. If it wasn't actually chosen by someone on the team, perhaps it came about because they used some kind of wizard to generate an application skeleton.