My change is not so much as a fix but a modification to generalize some things so just average common android or java developer can just reuse my projects template source and just change the text and go and output their project website.
Thus I changed the DocFile to instead look for website subfolders instead of the normal sdk folder layout when setting to output the cs files.
Starting at line 110 are my changes. Obviously, if someone wants a different subolder structure they might have to override something or add some additional head properties to some jd files. But, for the most part it gets them there as far as being able to pick up the project right away and reuse with minimum fuss or mess.