Have you ever used a Mac? No matter what you answered, there is an interesting concept that makes things a lot easier when it comes to installing and/or deinstalling applications. To install a new application, you just unpack it in the directory you want. To remove it, you just remove the folder. You can even move that folder to other locations and the program will keep running as well as before.
So what's going on here? While I'm not a Mac expert - in fact I still know very few things - I guess that applications use relative paths to their files. As an example, in the Unix world, the foo program could search for its pixmap in ../share/pixmaps/foo.png (starting from its respective bin directory), instead of trying to open /usr/local/share/pixmaps/foo.png directly. Using relative paths, you could move the program anywhere else: the relative paths do not change, while absolute do.
If you have understood this, you'd have noticed that it's a matter of removing the installation prefix from all paths, hence the name of deprexification. You can find more information in this article.
This sounds like a good idea, as it could certainly make things a lot easier when installing packages: just consider the distribution of binary tarballs for any system, no matter what their tree structure is. But it seems that getting there can be very difficult (if not impossible) :-/