Reorganized directory structure.

* Organized top-level directories by language rather than by
  functionality (because different functionality may be needed for each
  language or different conventions may exist).
* Updated contents to describe new layout.
Updated project organization guidelines after moving Java.
Improved, simplified Java build.

* Makefile now uses build directory for Java build
* Makefile is now more automatic, simpler to maintain
* Incorporates new directory organization
* Reordered JUnit JAR lookup to be local-to-global instead of
  global-to-local
Added build directory to ignorables.
Added Java documentation target to makefile.

* Added target for building Java documentation.
* Added documentation of main targets.
* Improved output of variable listing.
* Renamed clean targets to be easier to read and look like a group.
Added Java documentation directory to ignorables.
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.
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.
Merge branch 'dev/afbarnard' into dev/kboyd

Conflicts:
	java/src/mloss/roc/CurveData.java
	makefile