If you’re using Git to collaborate with others on GitHub, ensure that Git is properly configured to handle line endings.
https://help.github.com/articles/dealing-with-line-endings
Clarion needs to have the right kind of line endings or it is really not very happy. I think it is ok if you clone a repo but if you download a zip from github then you may have issues.
Here is an example from my Clarion Metro Wizard project. See the section # Custom for clarion