~/.(appname) vs. ~/config/(appname)
 

Inkscape moved their config directory from ~/.inkscape to ~/.config/inkscape, stating that this was the new trend for Linux desktops. What determines if an application should go in the root home dir versus going in the config dir?

A good read on this would be the lsb (linux standards base) which defines where files SHOULD go among other things. However, some distros and desktops change those locations to their own liking. I'd suggest reading your distros manuals (usually available through web browser) and manuals for your desktop.

Of course, some programs compile to unusual places which can sometimes be changed with configuration switches.

Tom

This is a very interesting topic; and generally there are LOT'S of schools of thought with regards to this.

In my opinion there isn't a place that an application should go but rather there are generally accepted practices for the different distro's out there.

Even with these, its very much a personal choice; I for example choose to compile and install my apps to a specific directory structure that I understand well - and is completely different to what people using Fedora normally would do :)