Look in the japlus file, they distribute a single file that contains linux, mac, and windows versions. Within this archive, are many folders including .bat files to launch JKA. Look in the japlus folder and you see the .so file (for linux), and a ton of pk3's. The pk3 that contains the server dll is "jampgamex86.pk3".
When you launch JKA and load a mod, it reads the pk3's in alphabetical order, so if you have like... "a.pk3", it'll be the first file open (provided you don't have any files starting with a number).
As far as your second thing, never "wipe" code away, if you only compile the jampgame, then you only need to copy that dll to your mod's folder, the game will load up the default dll's for the other two (UI and cgame). If you wipe, compile, and move the "empty" dll file over, you're for sure to have a failed mod.
And finally, CVS is a content management system thing that many groups use to collectively work on a project. It keeps all contributers up to date, and allows for additions to code across groups go alot smoother.
-- Griswald, RKR Project Co-Leader