The man pages[1][2][3] for the hier command on various BSDs are also worthwhile reads if you want to familiarize yourself with *NIX directory structures in general.
A lot of this is driven by historical concerns of large institutional installations that don't really apply to most Linux users today. We're set up for the possibility that /usr is a read-only NFS share for use by multiple processor architectures. This is an increasingly rare scenario, but it's the justification for why /var was split from /usr and /usr/share was split from /usr/lib.
It's bordering on unreadable at the moment. Turns out you can't just slam a bunch of advertising markup on top of a web page and assume it all works fine. Who knew.
I'll bet it's fine if you have ad-blocker and similar, but it's atrocious, bordering on unreadable, if you don't. If you write for the web, and you care about your readership, you need to look at your own pages with browsers they are likely to use, and no extensions. And with extensions as well, because while some of your readers will use vanilla browsers with no extensions, some will have heavily personalized setups.
Don't take it for granted that what you see is what everyone sees. It's just not true.
Rather than following the Filesystem Hierarchy Standard like most Unix-like systems, each program in a GoboLinux system has its own subdirectory tree, where all of its files (including settings specific for that program) may be found. Thus, a program "Foo" has all of its specific files and libraries in /Programs/Foo.
Separate directories do not imply conflicting versions colliding (which I guess it what you refer to?). In fact, I'd say is it less likely. Can you eloborate?
[1] http://www.freebsd.org/cgi/man.cgi?query=hier
[2] http://www.openbsd.org/cgi-bin/man.cgi?query=hier
[3] http://netbsd.gw.com/cgi-bin/man-cgi?hier