Update theory paper
* Bring back the Pedersen example as an example.
* Create section for availability.
-Added new studies test for folding logic
-Updated on_edge logic to find edges correctly
-Added on_edge information to netcdf file for visual debugging
-Added surface duct test within the refraction test suite
*Attempted to add a bottom duct scenario but was not successful in
implementing because the rays would not 'cooperate'
-Commented out the ifdef debug statements
-Removed the on_fold and detect_caustic functions. Rolled these logical
statements into the new and improved on_edge logic.

on_edges: now computes whether a point is on an edge and which of its
neighbors is too. Upon determining which, it then checks to see if it meets
the caustic criteria and then adjusts the data appropriately.
Merge branch 'documentation_changes' into development0.03