Removing logging

The logging mechanism, although useful, is being
in my opinion overly used in gapt. We shouldn't
use logging for debugging, and we shouldn't leave
debugging lines in the main repository code. Also,
making a class extend yet another interface is
really overloading its responsabilites and the
code is often harder to read with all the
debugging lines around. Another reason I can think
of for removing the logging from all these files
is the fact that we either need to keep a very
long (and constantly needing updates) log4j file
or we live with its warning messages.
For running the cut-introduction experiments, the
only logging that is left is the one in the test
script itself, and no other if I can help it.