Remove fog from the main scene in the 3d renderer 

I decided to completely disable the fog effect from the main scene as it
is irrelevant for a three dimensional plot and it's mostly useful for
cases where you want to give the effect of light faiding away as
distance increases. The alternative to this decision was to take the
matrix inputed in the commmand line interface and scale it to a proper
value, but this would increase the processing time and the fog doesn't
really add any value (qualitative) to the plots.

I added an extra script usage case where I added a pc file that I manipulated
to have big values. This should help us check for these "special" cases in the
future.

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For a much more detailed description of the changes, please look at the
commit message of cdce40d