@TheNiceOne: It would be simpler if everyone just put the INIs in the Data folder, especially if it is only one. Sort your Data folder by "type," no clutter, organized. Adding exceptions for every possible INI folder would be a pain. Also, I have not had to manually install the INIs from any mod I use yet. The only manual installation I have to do is put your price files in the Data folder (in the Enhanced Economy folder.) Why can't they go in Docs?...no matter....
I think some history is in order. A year (or a bit more) ago, a discussion started about ini files, and many wanted them in a separate folder. I started a thread about it, where people could vote for their preferred location. Options were the data folder, an ini folder, and a couple of other options I don't remember. The ini folder won by a very large margin. After that several mod makers, including myself started to use an ini folder for ini files.
Sometimes after this, someone else than Wrye (maybe PacificMorrowind?) added support for this folder in BAIN, and most people was happy. But then Wrye emerged and decided to remove the support for this folder because he had previously suggested and added a "scripts" folder for ini files. The fact that the majority preferred the ini folder, several mods used the ini folder and not a single mod used the scripts folder was not enough to change his mind.
So now we're in a situation where some mods use the ini folder and BAIN purges that folder during the install. There is also the case of Enhanced Economy's additional folder of course-
Okay, well I do not think the code should be super complicated with exceptions, but it would be nice if there were one folder, but there is...Scripts? If authors are conscious of BAIN, when not stick the INIs in there so that everyone is not just bickering. The folder is already there. (I had no clue and I have 20 INIs in my Data folder, directly and in subfolders.) You say that Wrye's rule gives modders trouble, but modders do not seem to be conforming at all either.
We did have a poll before we started to use the ini folder, so if anything, the ini folder is the conformant place.
The scripts folder is a bad choice, partly because it is much less descriptive than the ini folder, partly because people are used to the ini folder, and partly because several of the mods using the ini folder are not actively supported anymore.
I do not have not downloaded one, out all thousand plus mods I have downloaded, with an INI in the Scripts folder.
And I don't think a single mod is using it.
I understand this is a sensitive topic. Not because it would be any hard to add ini folder support to BAIN, but because Wrye disapproved of it, and I understand that the people who have taken over are reluctant to step on his toes.