Did the Devs just rewrite and add to previous versions code to add new things and features? or did they start from scratch and rebuild the game around the original engine code? Is what meant in my reply.
I really have no idea what this means so I'll just blab about how the game works-ish and maybe that will help...
Each thing in the game has an associate entity file with it (a simple text file)...each planet, frigate, capital ship, starbase, planet structure, technology, ability, etc....each has its own .entity file...additionally, abilities (and occasionally other things) can utilize multiple buff files...
Then you have the effects, meshes, and textures...each 3D object requires a mesh (the "frame") and a texture (the 2D "art" that covers it)...effects also have their own things that they require...
Rebellion utilizes some things from the original, but it's mostly concepts and art that it is utilizing...here is an example of what I'm saying: each planet entity file in rebellion has a section in it called "ruinDef" that specifies what happens when Stripped to the Core is used on that planet...you can't use your planet files from original sins, because they don't have this ruinDef section...so all the planet entity files are "new" in that they now include all the necessary lines that Rebellion requires...however, most of the stats are the same (and presumably copied) from vanilla...
Many entity files are like that...extra lines had to be added to the text files to accomodate for the new features of Rebellion, but it's not like every line of code was completely rewritten...the devs probably had a script editor just run through and add the new lines to their existing entity files...
There are 2 guesses I have for why these MDs are occuring...one is a memory leak, which can be the result of a weapon/ability particle effect or a poorly written ability...you won't necessarily get an error while the memory leaking is occuring, just a MD once you exceed the limitations on memory...an ability could be infinitely looping and applying infinite buffs, or a weapon effect could end up never "ending" as the "projectile" continues forever in space...each time the weapon fires, more memory is sucked up and the game eventually crashes...
There are other examples of these phenomenon and a whole host of other possible sources for MDs...
I don't know if this answers your question but I don't honestly know what you are asking...Rebellion is taking the old stuff and adding what needs to be added to pre-existing files...additionally, completely new files are needed for the new things that require their own meshes, textures, entity files, or particle effects....