Currently there is a annoying navigation problem in Workbench when developing mods.
All base game and mod code is merged into same ScriptModule and that makes navigation and separation of base game / modded code quite annoying to deal with.
This problem gets even worse if you have multiple mods overriding same file.
Example and this is even without base game extracted.
My suggestion here is add additional step in tree list.
->3_Game ->BaseGame ->Base Game Content ->Mod1 ->Content of mod 1 ->Mod2 ->Content of mod 2 ->Mod3 ->Content of mod 3
This would greatly increase Workbench usability for modders.