Refactor folder structure and convert to Maven

created the typical src/main/java etc folders (a bit tricky) and added
a pom.xml with a parent of scijava.

Only tested to see if it opens. I will be removing individual jars to
rely on maven dependencies only.
Created initial pom
POM: tidy up order of configuration blocks

This was accomplished using:

   mvn tidy:pom
POM: update to latest pom-scijava parent
POM: reorder dependencies alphabetically
AutoThresholder: remove non-UTF-8 friendly chars
Add REngine and rserve dependencies

This also updates some package references to match the version now
depended upon.
POM: fix jdom dependency version

Version 2.0.x has package prefix "org.jdom2" whereas we need "org.jdom".
POM: depend on the ImageJ public group repository

The advantage is that this transparently links to _all_ repositories on
maven.imagej.net, instead of _only_ the ImageJ releases themselves.
POM: add monte-cc and javaoctave deps
Fix jex.statics class imports
Fix references to miscellaneous.StringUtility
POM: use jar packaging for xadisk dep
POM: fix javax.mail dependency
POM: add swingx dependency
Restructure as a multi-module project
Add a toplevel application module

This module is intended to be a single dependency for anyone who wants
to depend on JEX, as well as a main method entry point.

It declares the core JEX library itself (jex-core) as a compile scope
dependency, and declares all the optional plugins as runtime scope so
that they are available (even though they are technically not needed to
actually build the code).
Isolate non-compiling code into "broken" module

Re integrate this non-essential code as necessary
Resolve bugs in Mavenizing process

Typo in main class name and pom groupID.
Resolve jdom version issue

We updated jdom version which resulted in alternative behavior from the
xml factory. It called element(name, namespace) with an "empty"
namespace instead of element(name). So our factory method now overrides
element(name, namespace) too.