...This warrants them to be placed on a seperate disc.
A2: The mega-texture style maps are mostly obj files as maps: and thus require the use of the newer versions of the engine: which are available in source codeform on the main disc; however the compiled version is usually updated for linux. The reason is that the older versions of the engine could not easily use an obj file as a map: since they contained no entities, also they were randomly scaled and rotated sometimes to a different version of "up".
The newer engine versions allow one to make more specifications using the file name of the obj model, along with other fixes for these types of maps.
A -quite ambitious- project to create a functional Doom source port in pure Java, trying to keep as close as possible to the original source code while at the same time streamlining it into a more OO and Java-friendly form.