I understand where you are coming from for Windows but on Linux this does not really happen. Everything ends up in a simple set of well known paths /bin or /usr/bin or /usr/lol/bin (soz) /usr/local/bin unless its ./sbin or perhaps some of those are symlinks. Now where's my config? /etc or /opt/lol/etc/config/tiddlywinks. Now go and find the logs. Oh the /srv and /var/lib thing and old uncle Tom Cobbley and all (and all)
OK, I'm taking the piss and actually it is surprisingly easy to find stuff on a Linux box once you work out the logic and the same usually applies on Windows too, especially once you find c:\programdata\ and the nether regions of your user home directory. Again the Linux equivalent needs a bloody great map (hello ~/.local) or some good grep and find skills to get around. At least you get those out of the box.