nice to see it evolving a little suggestion on the comp ability issue
i suggest creating a compaility node which looks like this
X would be an int
0 = generally compatible
1 = generally incompatible
2 = stand alone
you can chose multiple 0value mods to go with a 1value mod but no two 1value will go together and unless they are each listed in each others mod list, and a 2 value mod will only allow the mods from its mod list,
this should give enough flexibility for determining mod compatibility.
a nice 4value would be that it merges mods thus allowing all mods from the mod list to be chosen disregarding their individual compatibilities.
( someone on the forum is already working on that for master affliction and stormworld as far as i have seen)