Fixes for Darcy flow advection method

[jdannberg]

There are a number of features that should be added to make the new Darcy flow method work correctly with a number of different tptions:

• [x] Add a section in the manual that explains the equations, why this is useful, and what the limitations are.
• [x] Adapt the time step according to the Darcy velocity (source/time_stepping/convection_time_step.cc)
• [ ] Make sure we take this velocity into account when setting boundary conditions (function replace_outflow_boundary_ids in helper_functions.cc)
• [x] would a graphical output of u_f be useful?

[danieldouglas92]

Manual section added in PR #4769