In particular, removed DaCapo-specific tomcat classes from main dacapo.jar.

Addressed issue #3049886 (jython generates NPE with eager compilation) by updating to latest release (Jython 2.5.2).

Addressed issue #3056019 and related issues (fixed multiple system properties during actual benchmark iteration).

Added a template method with which to augment the system properties during the actual benchmark iteration.

Added a template method with which to augment the system properties during the actual benchmark iteration.

added small tool for helping process docs, added some blank docs and alterred build to construct documentation

moved the hoisted the harness bootstrap class out of benchmarks/harness/src into benchmarks/src and introduced a clean target

added the property dacapo.callback.classpath which can be used to specify the path for finding user defined Callback classes

Separated Digest into a separate library for inclusion in Tomcat and default Harness.
Removed dependency in H2 benchmark code on Config (and commons cli).
Top-level harness now loads classes through a separate class loader, which has a
common parent with the benchmark class loader, but is not itself an ancestor or the
benchmark class loader.  This isolates harness code from benchmark code.