I promise I really wanted to read all 352 pages of this thread (but didn't have 3 months of spare time!), and I was also trying to search for the answer (but I didn't find it), so sorry if this question was already asked and answered.
So, from what I know, there shouldn't be two .lua files having the same name in the mods, as they will be overwriting each other and causing issues.
I've just checked all the mods I have for lua duplicates, and I have found a few in the custom civilizations, hence my questions below:
1. In both JFD's Papal States and Commonwealth of Iceland there is the same file called CityInfoStack.lua. After inspecting with WinMerge I saw a minor difference - two lines of code more in The Papal States. Will it cause any problems to use them together, and if so which file should I use?
2. I have found a number of CultureOverview files in the civ mods. There are minor differences between JFD's Iceland and Papal States / France (player vs pPlayer code) - shall I just use the France file as the newest for Iceland as well?
On top of that these files are present in more civs. I can see that Luegi follows the same file construction as JFD's civs, but TPangolin (e.g. Mexican Republic) and Pouakai (e.g Argentina) have a different file construction - will I have problems playing their civs together with all the JFDs? Will they work if I choose JFD's file? And if not - any chance that you guys talk to each other and try to unify this file construction?