Changed project to work with Gradle.

* The classes are now in proper directories as expected by the Gradle's java plugin
* .classpath removed since it is created with 'gradle eclipse' if needed now.
* .project file is now managed by Gradle, hence the slight change in layout
* ClassUtils now uses Reflections to get all the classes in a package -- before we used a method that
  didn't get them if they were in a jar. And now we can run the program as a jar, so we needed a new method.

To build: gradle build
Added Main-Class attribute to jar Manifest
Updated README and jar name