Changing maven package for protein-comparison-tool to shade

Rather than copy all the jars individually using the maven assembly
plugin, we use the shade plugin to combine them all into a single jar
file, then assemble that. Since all our dependencies are
lgpl-compatible, this should be OK.

This fixes #197.

I've also included improvements to the run scripts which let you run
them from any directory, not just the current one. Maven handles
replacing the jar filename at assembly time.

Finally, I changed the name of the assembly. They are now named like
'protein-comparison-tool-4.0.0.jar' rather than including a timestamp.
Merge pull request #198 from sbliven/master

Changing maven package for protein-comparison-tool to shade
Removing warnings
More #111
Removing ad-hoc logger verbosity control
Fixing #193
- also some improvement for #191: now a TranslationException will be
thrown when compound not known
- a few improvements for other issues: #111, #155, #185
Merge pull request #199 from josemduarte/master

Exception handling and logging improvements, solves #193
started to work on a parser for Phosphosite data (data under CCBY_NC) http://www.phosphosite.org
upgrading to latest log4j
making access method public