DarkPlaces code is radically different from GLQuake/WinQuake. It has about 8 years of changes in it. (Last I heard, 97% of it is entirely rewritten from GLQuake).
For someone just starting to learn engine coding, it would be like skipping to end of an advanced calculus textbook without doing any of the middle of the book.
There is a lot of material in those Quakesrc.org tutorials and comparing an contrasting engines like GLQuake vs. FitzQuake vs. aguirRe Quake vs. JoeQuake is a good place to start.
If you really want to learn about EBFS, do the EBFS tutorial and the FrikFile tutorial.
Here is a very simple and generic ProQuake with EBFS added by RocketGuy that also has Frik_File ().
I've not used it, but RocketGuy runs it on his RQuake server so it must be stable.
Above and beyond that, the QuakeSrc.org tutorials are a great place to start because they help you understand.
If you want to try to understand DarkPlaces and the extension system, you'd probably be best off using WinMerge to compare different old DarkPlaces version back when DarkPlaces was far more similar to original Quake.
Like such:
http://icculus.org/twilight/darkplaces/files/2000/
I'd recommend #104
http://icculus.org/twilight/darkplaces/ ... ine104.zip