Adds "#define MPI_INCLUDED" to trick NetCDF.
Addressed weirdness with mpiexec and ssa python tests:
Call mpiexec without an absolute path and it inherits a PATH from the environment.
Call it with an absolute path  (/usr/bin/mpiexec) and you set the PATH to /usr/bin.
Our tests call mpiexec with an absolute path to ensure we use the correct version, but this means there is a path side effect.
Calling a python script with a shebang with mpiexec can then result in a different python executable being used than the user's standard environment would find.  If a different python version is picked up (e.g. 2.6 rather than 2.7), you can fail to find python modules such as PISM and petsc4py if they were compiled for a mismatched version of python. Consequently, tests fail.
Now any mpiexec calls in the test suite that run a python script actually run python explicitly, with an absolute path to the user's python executable. (i.e /usr/bin/mpiexec /opt/local/bin/python my_test.py rather than /usr/bin/mpiexec mytest.py)

Fixed bug in parallel SSA test reporting messages.

All SSA tests are now run in parallel.  Only prose was being run in parallel.  Maybe I unintentionally broke this last summer.
Language has been cleaned up in InvSSAForwardProblem.  We are technically inverting for some parameter zeta, and tauc=tauc(zeta) (e.g. zeta*zeta or exp(zeta) or just plain old zeta).  So InvSSAForwardProblem::set_tauc becomes InvSSAForwardProblem::set_zeta, etc.

InvSSAForwardProblem now allows zeta/tauc to be fixed at certain nodes (e.g. where ice is floating or absent).  This can be turned on for now in vel2tauc with the option -use_zeta_fixed_mask; this unhelpfully named option is going to go away soon when this feature is turned on by default.  This feature will be used for inversions in regional models, where tauc in the no_model_mask zone will be fixed.

plotting tweaks in vel2tauc

make_synth_ssa has new options: -misfit_type = grounded or fast to build a misfit functional based on all grounded ice or just the fast stuff (as determined by -fast_ice_speed)
changes concerning the ice schelf - bedrock interface
modification in CFBC when applied to a setup of an ice shelf confined in a bay of ice-free land avoiding the uphill creep of ice...
PISMIO -> PIO updates in a few python places
Housekeeping of python inversion code.

Lots of code from examples/inverse has been properly promoted to code in site_packages/PISM

The unholy examples/inverse/pismssaforward.py has been refactored and is dead.

Python "executables" vel2tauc.py and a few others are now installed in the PISM binaries directory.

Still more PISMIO->PIO fixes (including fixing some of my broken fixes…)
1) Added adaptive timestep based on CFL-criterion for eigenCalving rate. 2) Fixed a bug in iMcalving concerning calved partially filled grid cells (vHref<0). 3) Changed eigencalving option, so that only -eigen_calving_K is needed in order to switch on do_eigen_calving.
Fixes a minor bug in PISMNC3File.
Ref re inversion
Reverted eigen_calving option(s) and moved cfl_eigencalving and nuBedrock options to pism_options.cc.
Modified eigenCalving.

1) There was a discrepancy in calculation of H_average (with respect to
the old mask and the newly updated H field)
2) In the calculation of principal strain rates as offset-neighbor
average avoid taking into account margin cells, which are affected by
the inward scheme in SSA.cc
Modified EigenCalving.
Modified partgrid mass flux.

1) partgrid mass flux should symmetric at ice margin (in and out), also
for grounded margins
2) for floating ice boundaries next to ice free bedrock the flux should
vanish (that's a specific case butrelevant in regional ice shelf
simulations at PIK)
3) Minor changes in cfl_eigencalving routine
Comment a line in iMcalving.cc using the online editor.
Two refs for hydrology, in press.
Merge remote-tracking branch 'origin/dev' into dev
Minor fix in eigencalving for parallel calculation
Deleted line 238 in iceModel.cc.
Updated refs.