[FIXED JENKINS-7478] Correct Line Endings for Batch Files

Converted EOLs to /r/n for Windows Batch files and /n for Shell files.  The purpose was to fix issue [JENKINS-7478](https://issues.jenkins-ci.org/browse/JENKINS-7478)
It's better to use switches with an explicit "default" behavior.
Usage of external library (like @daniel-beck proposed) would be useful as well