Why would all of my files have duplicates with a '~' at the end?
The tilde files are automatic backup files of the last version created by the text editors. You can turn off this automatic creation by editing the preferences of the text editor you use.
Those are probably temporary / backup files created by an editor like emacs, vim etc. Anyway, such files would have nothing to do with git.
Conventially, the ~ suffix indicates a backup copy. It is usually created by an editor which saves a backup copy of the file (with the old contents) when you make changes to it. You area probably using an editor that does this.
I believe the convention to use ~ as a suffix for backup files started with a long time ago with emacs.