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Using attachments for the ET and SRBs is probably a good idea, although we'll need some way of controlling SRB gimballing, etc. The other issue will be transferring mass and thrust over to the shuttle vessel, but that'll be easy.
All can be solved, SRB gimballing for example over a standard serial bus interface.
The main problem I have with using static libraries are that it'll be difficult to split the subsystems up into distinct libraries. For example, a lot of libraries will need to communicate with the power systems library. Also, a lot of this stuff will be fairly shuttle-specific, so it wouldn't be useful for other vessels.
Yes, the libraries would depend a lot on each other, but would be just split for reducing build times - currently, any changes to the Atlantis.h results in effectively a complete rebuild. And when something is changing in the subsystems, this also affects a more source files than needed.
I don't think the subsystems are all very Shuttle specific, and even if they are, they are often having enough similarities to other subsystems of that kind that refactoring them into more general classes is no large effort. I did a rough comparison between Space Shuttle and Gemini, the general kinds of subsystems are almost the same, only number and specific model varies. Building a Gemini simulation from SSU code would be not that much work anymore.
The RMS/MPM systems create the additional visuals in the Realize function; this should work for other subsystems.
Yes, but some more stability for handling the meshes would be good. Currently, it works best when there are slots for the additional meshes reserved, which means you need dummy meshes if something is missing for filling the gap.