Hello Nick,
I wanted to personally reply to your email and request seeking permission to use our copyright for non-profit, educational reasons; or, perhaps modifying the entry so as to not infringe our copyright.
We wrestle with requests like this often and unfortunately we can not permit either while still protecting both our copyright as well as our partners.
I am sorry. We don't like having to say this and realize that to some in the development community this makes us look like the 'big, unfeeling corporation' totally out of touch with what fans and very talented developers are trying to do. (Which I assure is not the case.) There are many issues at play here but at the core is that were we to leave the game on JAVA4K.com there would no doubt be tens of thousands of play sessions of that free and unauthorized version at the expense of the commercial and ad-supported versions that are available officially, which are thus non-infringing.
Boulder Dash(R) is a highly valued Intellectual Property, which we still very actively exploit and we must do what we can therefore to be sure that we do not take any action that could be referred to as letting the game lapse into the 'public domain'.
As for trying to outline how you could modify the entry so that it did not infringe upon our copyrights: that is not something we would dare venture to do. Copyrighted materials does not lend itself to that sort of analysis.
Again, I am sorry. I know this is not the answer you were hoping for; but, we simply can not make an exception or set a dangerous precedent.
Best wishes for your other endeavors,
Richard
I was not given permission to use their copyright

perhaps i think it was markus's ~20000+ plays for his VVVV entry that scared them

Ah well.. with my first baby due later this month, i do not think i will have time to overhall the game to make it not infringe

If some one else is interested in taking ownership i can give them the source code, and tools i made for level data and image data generation.