Mac/Linux sharing files to Windows users on github: problems with new lines

Dear Mac or Linux users,
I am trying to share capture-recapture R source code and JAGS models on
Github.
I am writing the scripts in Emacs on a GNU/linux Ubuntu machine. When
Windows users download my scripts, they get a single line of code (no line
breaks) and the JAGS models fail. What is your best-practises for getting
*nix scripts to work and read properly on Windows through Github?

I am using the program unix2dos (in the ubuntu repositories) to convert the
*nix line-breaks to the Windows line-breaks, and this seems to work when I
download from Github and open on a Windows machine with notepad or
notepad++. However, other Windows users still can't get the JAGS models and
R source code to load properly.

Here is my github directory for windows:
https://github.com/faraway1nspace/PCRD_JAGS_demo/tree/master/WINDOWS

Can any Mac or Linux user share their workflow?
Thank you,
Robert

"You could give Aristotle a tutorial. And you could thrill him to the core
of his being ... Such is the privilege of living after Newton, Darwin,
Einstein, Planck, Watson, Crick and their colleagues."
-- Richard Dawkins

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