What line endings to use for cross-platform compatibility?
I think the best option is to let your users decide. Give them a dropdown box to choose Windows/UNIX/Mac style line endings. You can keep the files normalized to UNIX style endings since they are the easiest to work with.
I am not sure if you can generate text files with a universal style of line endings. Most tools like git normalize their files and leave the users to configure which style of output they prefer. Jeff has written a great article on line endings which goes into some historical context.