For mobility and to potentially enable chroot down the line, the directories now created under /etc/koha/sites and /var/(spool|lib|lock|run|log)/koha should be created under a common directory. I'd be happy to contribute a patch if a good common path can be found.
I'm not convinced that debian would let us get away with that. Also, /etc and /var are the appropriate places for what goes into them. This said, it wouldn't be the end of the world to symlink them together, so they still appear like they are now, but everything is really under /var/lib/koha. Additionally, it would only really need to be /var/lib/koha, all the rest are transient data. Not completely sold on the need for it vs. the additional complexity though.
Fair enough! :) Here is a patch in case it's helpful to others looking to move instances around, or to give hosted catalog customers limited shell access.
Created attachment 10716 [details] [review] Patch storing all instance folders under /var/lib/koha/instance name, with symlinks
Patch is not a git patch, reformatting now
Created attachment 11819 [details] [review] Bug 8310 : Patch to store all instances in /var/lib/koha - For use with the debian packages
As I understand it, candidate packages for inclusion in Debian must use the standard Debian file layout, as in the current packages. Therefore, I would suggest the patch is probably not suitable for inclusion in Koha master, though the patch might be useful as an option for people running their own hand-rolled packages.