Ungh, Ubuntu as a server. Leaving that aside, simply use the package manager (something like Synaptic in the GUI) to check where the files for the rt package are installed. Back those up if you have concerns about possible customizations done to core instead of local code. Backup your database. Then:
A) Update your system to something more modern, and install the corresponding rt package B) Download the source tarball from Best Practical, and follow the enclosed directions P.S. /opt/rt3 is the default path, for some reason several distributions like Ubuntu like to shove stuff under /usr/local/packageName and give users longer pathnames to deal with. Discover RT's hidden secrets with RT Essentials from O'Reilly Media. Buy a copy at http://rtbook.bestpractical.com