Remove settings package; Cleaned up messages file

[drewejohnson]

Wasn't a need for the settings directory, so it has been refactored out. The following files were moved, in reference to the root serpentTools directory

1. settings/__init__.py --> settings.py
2. settings/messages.py --> messages.py
3. settings/variables.yaml --> variables.yaml

The setup.py script was modified to remove the serpentTools.settings package, and move the variables file to/from the correct place upon install.
All calls to the settings package, i.e. from serpentTools.settings import rc still work, but the message imports had to be modified to point towards serpentTools.messages. The latter change is the cause for most of the files being modified

Changes to messages.py

There is not longer a single error function with an optional fatal argument. There is now the error and critical functions. The difference is that error should be used if an exception was suppressed internally, while the critical function should be used in the event of a serious failure. Perhaps bundled inside the SerpentToolsException class?

Also, the now correctly named deprecated decorator takes an argument on use.

@deprecated('alternativeFunc')
def foo(x, y):
     print(x * y)

foo(1, 2)
WARNING : serpentTools: Function foo has been deprecated. Use alternativeFunc instead
DeprecationWarning: Function foo has been deprecated. Use alternativeFunc instead
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