As was previously warned, I just patched the kernel to remove particle indexes. All the modules in svn are fixed so that they compile except for em, which didn't compile anyway.

The changes to be aware of are: - Particles now have names which are strings identifying them (Particle::get_name, Particle::set_name). You should use these when you print particle-related error messages. - Particle::get_index goes away (it is currently left there for backwards compatiblity, but will really go away next week. Domino at least needs to be patched for this). - Model::get_particle(unsigned int) goes away (likewise, it is left in for backward compatibility until next week. The current implementation is linear though.) - the IMP_LIST_IMPL macro takes another argument, so just add a comma at the end if the compiler complains at you