I am using luadoc and running it on Unix and windows, unfortunately the output is different on each system because of the DOS/Unix line endings, this really confuses my source control as it thinks every file has changed (mercurial). How can I make lua use one or the other?
I know nothing about lua, but you might want to solve this at the SCM level, Mercurial has the EolExtension for that.
That being said, you're probably missing some feature of luadoc.