Added Java package (JAR) target to makefile.

* Added makefile target for public javadoc.
* Added makefile target for Java package.  JAR includes readme, license,
  source, bytecode, and public javadocs (for library only, not tests).
* Updated README to include information about the Java library and
  package so that someone downloading the JAR has a place to start.
* Made README clearer and more readable as a text file.
* Moved Java testing targets in makefile.
* Added reference for JARs.