Adds warnings about missing tools required to re-build docs.
Removes the -pdd_annualize option altogether.

Now that the PDD code is fixed (I hope) we don't need the "annualized"
version of the PDD. "Normal" version produces equivalent annual
average mass balance and does not interfere with time-stepping and
periodic forcing.
Adds missing begin/end access calls.
what should be the defaults for porosity?  these are a revised guess; the sum phi+phi_0 controls the timescale contrast between CFL and the pressure diffusion update
Update PDD tool

Added Calov and Greve formula, time-series interpolation and choice of integration method.

The regression test still fails and for a reason; I am going to open an issue about that.
More fixes in the PDD code.
Update of Test P to match current version of manuscript and current version of Darcy flux relation with 'k'.  The issue that Test P uses an unrealistically low conductivity of ~10^-6 remains; compare k=0.01 in Schoof/Hewitt work.  Fixes regression test for Test P.
Merge branch 'dev' into hydro-fix-k