Remove unused variable from documentation.
Minor changes in loglevels.
Re-add unused commandline argument.
Move microscopy related stuff into a new package 'MicroscoPy'.

This is mostly for being able to also use it from within Jython which is
lacking the NumPy and SciPy packages.
Use full module name for 'os.path'.
Add workaround for bug in Fiji+Jython.
Use workaround for exists() bug in Jython+Fiji.
Adjust sample data links to re-structured packages.
Split out MicroscoPy parts of imagej module.