If I understand your issue correctly, here is an article with a terrific graphic that shows how various feature modules can be brought into a product release. Your widespread files, with their own enhancement paths, are the feature lines in the graphic.
Unmonitored folders: Yeah, I wouldn't like it to keep saying certain things are not tracked. You can add use .gitignore to exclude those folders. There are other ways (.git/info/exclude or local, global ~/.gitignore), but this is probably the best way for what you describe, because it's