Got Java documentation off the ground.

* Expanded javadoc target in makefile.  Changed to generate private
  documentation useful for internal reading and checking javadoc
  comments.  Javadoc for packaging will now need to be generated
  separately.
* Created file containing javadoc options and boilerplate text.
* Created overview documentation that appears as part of the initial
  javadoc view.  The generated overview file must be patched due to a
  javadoc bug.
* Created package documentation.
* Revised and added javadoc comments to classes, including HTML markup.
* Added private constructor to Arrays to prevent Java from generating a
  default public constructor which was then appearing in the javadoc.
* Added to ignorables the directory of files that javadoc includes
  because the only files there are generated.  That could change.
Removed unnecessary access to fields.

* Improved principle of least privilege.
* Improved future compatibility of API and so prepared API for release:
  can always increase access but not reduce access due to backwards
  compatibility.
Created generator of figures for future ROC/PR tutorial.
Started file of references.
Updated copyright years on recently-modified files.