Moved cfg from profiler.py to projConf.py.

Features added with the new projConf.py:
 - get() wrapper function for convenience
 - normPath() transforms any relative or absolute path to os specific
   format
 - getPath() calls normPath(get()) for convenience
 - Two parser functions for convenient file reading of Config.txt
   and index.txt.
 - invokeNeuroConstruct() which is awesome in the way it does just this
   one thing, but well.
Total rewrite of Multi*.py using class inheritance

The new implementation will be easier to read and reduces code
duplication a lot.

Also used the new logger, created by the profiler.py module using
profiler.getLog().
Heavy modifications to analysis, chromgen, fitness

Made many small modificatons using the functionality of profiler.py for
logging and projConf.py for configuration management and uniform
handling of input (via get(), getPath() and parse* functions).

Total removal of any BS == 1 checks and most files are opened with the
safer "with" construct (auomatic file.close() call on exit/exception).
Added *.pyo to .gitignore

*.pyo files are created by invoking the python interpreter with -O and
are optimized variants.
Added documentation to profiler.py and README.md.