relax SVN archive

Created the GUI interpreter object apply() for synchronous calls to the user functions.

Redesigned the GUI interpreter object so that the thread is a separate object.

This is to allow both synchronous and asynchronous calls to the interpreter in the future.

Added the _get_uf() method to the GUI interpreter object for abstracting the code.

Fixes to the unit tests for the PyMOL and Molmol macro user function renamings.

Fix for the molmol plot sample script for the pymol and molmol write to macro_write rename.

Fix for the user manual LaTeX longtables for the pymol and molmol write to macro_write rename.

Fix for the dauvergne_protocol auto-analysis for the pymol and molmol write to macro_write rename.

Improvement to the PyMOL model-free macros - bonds rather than atoms in selections are now coloured.

The backbone oxygen is no longer shown in the PyMOL model-free macros.

Decreased the amount of time waiting for PyMOL in pymol.macro_apply to 3 seconds.