A. The files you are modding (in correct folder locations). Exactly what files this has to be depends on what aspects of the game you are modding.
B. For Entrenchment/Diplomacy, you must include an editted entity.manifest file if you added any new files.
That's about it actually. If you are just editting the stats of existing ships for example all you need to do is create a new folder in your mod folder, then another folder inside of it called GameInfo, then put the editted ship entity files inside that folder and it should be good to go.