Modding Cpanel and preventing overwriting when upgrading
I have just finished modding cpanel's x2 theme and some mods to the horde theme too. These include things like making my website name appear in the window title bar rather than cpanel, redirecting people directly to the main horde login from the first cpanel page rather than going to the annoying "please choose your webmail program page" first, deleting some of the information boxes down the left side, etc etc.
Obviously I want to keep these changes and not have to keep maing them everytime I want to upgrade the cpanel software to the latest version.
I know how to prevent files from being overwritten but my concern then is that in installing an upgrade I will end up with a duff installation because potentially I could get a half baked upgrade because I have made some files un-upgradeable.
Any ideas how to get around this problem?
the obvious solution is to not upgrade I know, but then I end up in security troubles.