Fix serious issue with bash scripting and java classpaths.

* The template expects classpaths to be specified in unix style
* If in the cygwin environment, the bash script will
  - Fragment the classpath (by ':') into components
  - run cygpath -w on each component, to ensure we have a valid windows
    path
  - Reconstruct the classpath, using the separator of ';'
* Ensure cygwin tests pass.
Adding a lame test for cygwin bash scripts.