My first commit using git.  Bringing most of the 2014 changes...

Short story.  ED: added a few tweaks/controls for mortality and reproduction, and changed
the disturbance routines so disturbance types are more descriptive, and forestry is now
consistent with the disturbance rates.  ED/BRAMS: the model can now be compiled without
MPI.  BRAMS: created a LEAF-4 that looks very similar to big leaf ED, and fixed CARMA for
shortwave.  Ramspost: fixed a bunch of things, added more variables.

Long story.
1. ED
   a. Changed minimum height for reproduction for tropical trees, based on
      Wright, S. J. et al. 2005: Reproductive size thresholds in tropical trees:
         variation among individuals, species and forests.  J. Trop. Ecol. 21, 307--315,
         doi:10.1017/S0266467405002294
   b. Bug fix in growth_balive, living tissues wouldn't be built again when
      phenology_status was zero (leaves fully flushed).
   c. Changed minimum reproduction size so that seed_rain actually works.
   d. Bug fix in rk4_derivs.f90, a call for qslif8 was incorrectly passing specific
      humidity instead of pressure
   e. Density-dependent mortality: Single maximum carbon balance, assumed to be equal to
      plant at the top of the canopy and no soil water limitation.  Added an offset for
      negative carbon balance mortality, so rates don't start hiking before reaching
      negative carbon balance.
   f. Changed compilation instruction files so it allows to compile the code with two
      different levels of optimisation.  This dramatically reduces compilation times for
      ed_state_vars.f90 and average_utils.f90 using ifort-13.  Old include.mk.opt files
      should still work.
   g. Added include that works with Embrapa computers.
   h. Disturbance routines:
      i.   Changed the land use classes in ED.  Now there are 6 categories
           1 -- Agriculture (cropland/pasture, still not split)
           2 -- Forest plantation
           3 -- Tree fall
           4 -- Fire
           5 -- Abandonment
           6 -- Logged

           This eliminated some redundant variables, such as plantation,
           nat_dist_type, nat_disturbance_rate since these patches are tracked and
           can coexist in the same site.

      ii.  Simplified the forestry routines.  Now the files in forestry.f90 only
           determine the rates and harvested area.
      iii. Harvesting now takes the minimum DBH into account for all logging.  The
           minimum is set a the land use file as before, but now it is also used
           during logging with biomass target (aka George Hurtt's files).
      iv.  Bug fix in disturbance.  Now if the disturbed patch would become too
           small, the entire patch is disturbed, so it preserves total area.
      v.   Disturbance rate in the output is now consistent with the patch
           creation.  This wasn't true for logging.
      vi.  Patch fusion now allows different disturbance types to be fused as long
           as they are sufficiently old.
      vii. Disturbance rates are now updated annually, to ensure that the rates are
           consistent with patch dynamics.

   i. Fixed utils_c.c so the string length is consistent with the rest of the
      code.  I had to hardcode the length, so this will likely happen again if
      str_len is changed.
   j.  Increased the maximum number of files so the model is able to handle
       the harmonised land use data sets.
   k.  Some other minor bug fixes, I don't remember all of them.

2. ED + BRAMS
   a. Turned all files that use mpi into F90.  This allows the code to be compiled without
      MPI support.  I had to do this to be able to compile at USP, I couldn't have a
      consistent set of HDF5 + MPI with the same compiler.  Somehow gfortran didn't want
      to compile MPI, and ifort didn't want to compile HDF5.
   b. Added several components of the vegetation water and energy cycle to BRAMS output. I
      haven't tested with ED-BRAMS yet, so beware that this may need some fixes in the
      future.

3. BRAMS.
   a.  Radiation.  Vegetation radiation is now solved using two-stream, based on
       ED-2.2 (check my dissertation).  It assumes 6 layers for numerical stability.
       Some of the parameters were borrowed from CLM-4.
   b.  Transpiration/photosynthesis: sun and shade leaves were determined from CLM-4
       formulation, and the photosynthesis for each of the 2 layers are solved using
       the ED-2.2 method (check my dissertation).
   c.  Root and growth respiration: similar to ED-2.2, root biomass is estimated to be
       the same as the leaf biomass.
   d.  Heterotrophic respiration: the dependence on soil moisture and temperature is the
       same as ED-2.2.  The maximum rate is defined after
       Reichstein, M. et al. 2003: Modelling temporal and large-scale spatial variability
       of soil respiration from soil water availability, temperature and vegetation
       productivity indices. Global Biogeochem. Cycles, 17(4), 1104,
       doi:10.10292003GB002035
   e.  Heat capacity is now based on biomass, like in ED-2.2.  The SLA profile was taken
       from CLM-4.
   f.  Thermal conductance and fluxes between snowy ground were updated to what is done
       in ED.
   g.  IADVEC=2 is now saving fluxes properly and STILT runs with IADVEC=2 are conserving
       mass.
   h.  CARMA is now working for shortwave radiation, and results are much more realistic
       than Harrington.  Cumulus feedback is also working with CARMA, and CARMA now
       calculates the direct/diffuse components of PAR and NIR.
   i.  LEAF-3/LEAF-4 have time steps for vegetation.
   j.  Additional variables to reduce nudging near the surface.
   k.  New RAMSIN variable to decide whether to search for LOU recursively or not.

4. Ramspost
  a.  Several new variables needed for the USP/LNCC project.
  b.  Several bug fixes in Ramspost, now Ramspost is working for pressure level
      coordinates and all vorticities and divergence are working.
  c.  Categorical variables such as soil texture and vegetation class are now reprojected
      using nearest neighbour instead of horizontal interpolation.
  d.  Removed "entry" methods to define sub-routines.  All sub-routines are now defined as
      independent sub-routines.

5. R scripts
   a.  Several bug fixes, updates, etc.
Added more ignore rules