Remove PySE documentation from TraP documentation.

[HannoSpreeuw]

Currently, the TraP documentation includes useful information on how to run PySE standalone.

But if we were to modify or expand some of the command line arguments, e.g. if we would add the option of exporting source parameters to an hdf5 - currently only csv is supported - file to the pyse.py script that would not automatically be propagated to the PySE documentation within the TraP documentation since pyse.rst would remain unaffected.

So pyse.rst should become part of the PySE documentation and be removed from the TraP documentation.

[HannoSpreeuw]

Preferably embark on this issue after the documentation_through_Sphinx branch has been merged, this might take a few weeks.