Well, I have just spent an entire weekend using Windows, amounting to probably more hours than I had spent with this operating system in the previous six months! Of course, this meant that I had to endure loads of automatic updates, their drain on bandwidth and automatic restarts! It was worth it though to get the Subatomic Particle Simulator up, working just as well as it does on GNU/Linux! It's nice to know that I've made this thing cross-platform.
More good news: In the process of porting the code, I realised that the best thing to do was to fork the Source SDK repository on GitHub, and that way avoid all the problems of contaminating a working copy to compile the simulator. It is here, so you can now clone it in a ready-to-compile state, or even download a ZIP file if you would prefer.
Again, same legal restrictions apply - due to incompatible licences, it is not currently possible to (legally) distribute binaries. Once again, I apologise for this, and hope I can sort it out in the future.
PS. If you would like to express your opinions on how legal restrictions like this should apply in the future, please go to this new campaign website.