iirc gtkradiant does that for you. A .pk3 file is nothing more than a zip file, so it just bundles all the files necessary for the map. Open some other map.pk3 with 7zip (or any other zip program) and check out the structure. Map .pk3 files should contain a .map file, a .bsp file, sound files, texture files, .script files. To compile gtkradiant, install scons, and run scons in the directory where youve downloaded gtkradiant, but if youre not used to compiling programs yourself youre gonna need a lot of google.