NOTE: I didn't write the bulk of this code. Most of it was taken from the source of the original Mods Folder.jar by ModGuy, which comes with the loader, found here.
I might be in a minority here, but there have been many times where I've ran my Mods Folder.jar, and it has reset all of my folder orders to default alphabetical order. No one else seems to care about this, so I decided to make my own version of it that only appends lines to the CharacterFolders files to correspond with new folders, and doesn't do anything otherwise.
TLDR: It doesn't mess up the order of custom characters and folders in the loader.
Please note that this won't fix folders that are broken. For instance, if you have a character folder, but you want to change it to a directory, even if you change all the files correctly, this program wont automatically update it.
The most recent version of the Loader that this has been tested on (Although this shouldn't matter) is v5.45c.