Hi Eric,
Thanks for your compliments and questions. For files without file extensions, I am not sure how you would list them, because Jomla's JFolder::files function uses PHP's readdir function to list the files, and it seems as though if readdir finds a file without an extension, it replaces the first character with a dot. That seems to be its standard procedure. I can't change that. I would have to write code to specifically handle that, or maybe even write my own version of JFolder::files to handle it. However, what kind of files are you listing that don't have file extensions? Files available on a web server should have file extensions.
Honestly, I don't quite understand your second question. If you asking about automatically having the listing expanded, either change Collapse Subfolders to No in the Plugin Manager, or set collapse='0' when you place it in the Article.
Hope this helps.