Is there a file or menu that will let me change the settings on how to deal with line endings?
There are 3 options:
The normal way to control this is with
git config --global core.autocrlf true
For details, scroll down in this link to Pro Git to the section named "core.autocrlf"
If you want to know what file this is saved in, you can run the command:
git config --global --edit
and the git global config file should open in a text editor, and you can see where that file was loaded from.