This shouldn't be an issue. Files that have CRLF line terminators should work just as well as those that don't. I tested a file with the old Dos style CRLF line endings on my production webwork 2.17 server, and the file worked fine with no warnings or errors.
Although, it seems something has changed on the develop branch and files with such line terminators are not working. I will probably need to fix that.
In any case, it is probably time that you convert those files to proper unix style line endings. Eventually, we are going to stop trying to support such stupid line endings. The only operating system in the world that has ever worked with CRLF's is Microsoft Windows, and even Microsoft is finally fixing that. It should be pretty easy to find a tool to do this. On linux you can use the command line utility dos2unix (available on Ubuntu in the dos2unix package).
Although, it seems something has changed on the develop branch and files with such line terminators are not working. I will probably need to fix that.
In any case, it is probably time that you convert those files to proper unix style line endings. Eventually, we are going to stop trying to support such stupid line endings. The only operating system in the world that has ever worked with CRLF's is Microsoft Windows, and even Microsoft is finally fixing that. It should be pretty easy to find a tool to do this. On linux you can use the command line utility dos2unix (available on Ubuntu in the dos2unix package).