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Couple things I thought of. Most importantly items in JA are static[...]

There are also upsides to them being static. It would be ridiculously difficult to compare them if they were not static, not to mention keep the specific data about every item... this is not the purpose of the feature being discussed here anyway, and is probably best left for coders with significantly more experience than me.

From a design point-of-view though, I can tell you that such a thing would be a serious headache for both modders and players...

For which we have... COMBO MERGES! Or should I say... "HAVE HAD COMBO MERGES SINCE JA2 CAME OUT!"

Available in a local store near you.

Yes, that's already been brought up a few times here, and will probably be the chosen interface if I can figure out how to make such a pop-up from scratch. I extended the assignment pop-ups to include Facility assignments, but I was building on top of an existing pop-up system then. I might have to copy The_Bob's work somehow to get this functional. It's a purely technical matter though, shouldn't be too much of a problem.

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For example I added a RAS bipod and a gripod and got a bipod bonus of 100% because the attachments were not mutually exclusive (oversight) and the bonuses (spell?) stacked.

Yeah... how does that have anything to do with what's being discussed here though?

Any limitations of the attachment/merge system are not relevant here... the transformation feature is exclusively meant to deal with items changing on their own, rather than as a reaction to other items attached or used upon them.