OSX, because of its big corporate watchdog, and the separation of the 'GUI' layer and the unix layer, has the cleanest directory structure by far IMO. Most of the times you don't even need a manpage or google to find out how to repair a misbehaving application - just delete its plist in ~/Library/Preferences, possibly also its ../ApplicationSupport directory. The OSX defaults system is so well designed, every time I need to do support on other systems I just ask myself why not every OS works this way. I can understand why Linux is the way it is and I like that too (for other reasons), but it at least shows why the Windows Registry is such a bad idea.
Why can't I reply to some comments? That comment about the new sandboxed folder structure made me realize he's right. What's going on with all those symlinks inside the container directory?
This just shows to me what a bad idea sandboxing is for those kind of apps that are supposed to interoperate with the whole system. Is there even a security benefit vs. pure unix permissions if you sandbox the filesystem but then you link in tons of crap that could be potentially attacked?
It's to do with comments that get deeply nested quickly, presumably to prevent back and forth flame wars and the like. If you really want to reply to such a comment, click "link" and there is a reply link on the that page, or just wait.
There is no question there is a need to have a place that "plebeian users" can't access. IMO, dot-files and dot-directories are as good as anywhere.