I have not seen a lot of discussion of organizing code files in coding literature, probably because many people use frameworks which take car of this for them. I'm curious to read about what others are doing and thinking in this areas.
The question regarding the order in which UNIX sorts various leading characters in an alphabetical sort relates to my site organization, particularly regarding the directories that hold key files like classes and includes that I have to get to regularly. If I can name these directories so important ones, like classes, show up at the top of the sort and less important toward the bottom, it makes it easier to find what I am looking for. Getting files into directories is also helpful as there are a lot of free files floating around and making it hard to find files like the index file that has to be at the root of the directory.
Hope this clarifies my question.