This article refers to Koha 1.9.x and Koha 2.0.x. For Koha 3.0.x this functionality is built into the installer.
The first step is to get a copy of the koha tree from CVS; there are directions for how to do this on the CVS section of Koha's SourceForge project page. I will call this directory <cvs>. For example, mine is currently at /home/mike/cvs/koha , Thus, if there is a script at say /home/mike/cvs/koha/script.pl, I will refer to it as <cvs>/script.pl .
You also need an installed copy of 1.9.x (I am pretty sure this process will also work for anything up through the 2.0 series, but I am not positive that there will be no major changes in the filesystem layout). I will call this directory <inst>. For example, mine is installed at /usr/local/koha. In this document, I will refer files(/directories) such as /usr/local/koha/intranet as <inst>/intranet.
In order to run these commands, you may need to run as root. Also, <cvs> and its contents need to be readable by the user under which apache runs.
Please note that I am not totally positive that doing things this way will not introduce any new problems. I run this on my system and have not found anything wrong, but I make no guarantees. If you see anything wrong or know how to improve this document, feel free to either change it yourself or send me an e-mail at mwhansenAThmc.edu. Thanks.
Barring any major problems, you should have successfully updated your install of Koha to use the most current versions of the scripts/modules/templates available via CVS. Good luck with testing!