If I start a new distro (e.g. LFS):
But, before you down vote: I've been asked to make a new distro for a specific project which they need (actually, want) a new directory structure with a few changes, for example remove the var and bin directories, but without halting the system. The application of this distro is so limited, so i think it shouldn't be a big deal as they need just a few packages to be installed.
These are few pointers that come to my mind and definitely it is not complete:
PATH should be updated in the startup scripts like ~/.bashrc, /etc/profile.d, and so on to reflect the updated directories./var quite often. (/var/log, /var/tmp) You'd need to modify all these location references./sbin/init which is going to start the initialization at /etc/rc.d or equivalent. If you start tracing all the scripts and services invoked in these startup scripts, I believe you should be able to capture all the places you'd need to modify the path names.