When submitting a hadoop job from Windows (Cygwin) to a Linux hadoop cluster (or vice versa), and when you specify multiple additional jar files via the -libjars flag, hadoop throws a ClassNotFoundException for any classes located in the additional jars specified via the -libjars flag.
This is caused by the fact that hadoop uses system.getProperty("path.separator") as the delimiter in the list of jar files passed via -libjars.
My suggested solution is to use a comma as the delimiter, rather than the path.separator.
I realize comma is, perhaps, a poor choice for a delimiter because it is valid in filenames on both Windows and Linux, but the -libjars flag uses it as the delimiter when listing the additional required jars. So, I figured if it's already being used as a delimiter, then it's reasonable to use it internally as well.