We allow people to define custom CSS templates for varying things - opac, intranet, and (hopefully soon) slips and notices. It makes sense to have a sanctioned place within Koha to keep those files.
I propose the following location:
OPAC - koha-tmpl/opac-tmpl/prog/custom_css
Intranet - koha-tmpl/intranet-tmpl/prog/custom_css
Additionally, it would be nice to update the packages to dump these folders into the backup, to save any custom files stored there.
We should also take care to *never* clobber anything in this directory on upgrade. We could provide "sample" CSS files (notices.sample, receipts.sample, to name a couple) but never overwrite anything else in that folder.
Documentation for administrators should also be updated to tell system folks the "proper," "best practice" or "suggested" location to keep custom CSS files. The path to external CSS files can still be defined in the syspref, so administrators can define an external server if they so choose (many need this functionality because they have no shell or ftp access to their server).
Questions? Concerns? Things I have not considered?