If you hit the generate index now button with nothing in the Folders Included box, it will create an index file in every single one of your folders. If you have a lot of folders, it can be quite a bit of work to go in and remove these files manually. This would make this plugin easier to recommend to new users.
If you want to (and you're on linux or mac) you can run:
find . -maxdepth 100 -type f -name '_Index_of_*.md' -delete
in the terminal and it will go through and remove them all
If you hit the generate index now button with nothing in the Folders Included box, it will create an index file in every single one of your folders. If you have a lot of folders, it can be quite a bit of work to go in and remove these files manually. This would make this plugin easier to recommend to new users.