Merge branch 'master' into Gab
Filename / function clean up

No functional change - just a clean of file names and the distribution
of functions between and within  files.
Added spatial functions, global DS read routines

Added existing functions from independence work for spatial grid
interpolation, surface area calculations and read routines for HadCRUT
and GPCP.
Reorganising

Essentially just a renaming of files and functions to improve
distinction between single site and other experiment types (1D/2D),
including in testing scripts.
Bug fixes after renaming

Renaming from last commit was incomplete, now test cases run.
Netcdf4 and plot resolution

Changed from ncdf to ncdf4 and increased resolution of plots. For some
this means that text scaling will probably be needed.
New timing functions

Allowing monthly, daily, annual data with time units of seconds and
days.
First working regional Aus plots

Changes that allow firs regional 2d plots
First regional plots for multiple benchmarks
Additional regional analyses

Added SD, RMSE, Correlation plots
Improved error reporting and added metrics

Metrics now reported for gridded Aus
improved benchmark error reporting
error field now not returned to javascript in file list unless there is
an error
Added units to plots
Metrics from single site analyses and font resize

Now all analyses, including single site analyses, report metric values
when they do not fail. Adjusted font sizes and font sizing approach in
single site analyses.
All active scripts now use ncdf4
Make getMonthDays 10x faster
Lat/lon reading fix for single site analyses

Lat/lon checking routine used to fail when lat(x,y) rather than
lat(lat) in netcdf file - now only a problem if the number of unique
lat values does not equal x or y (i.e. non lat-lon grid).
Reworking EmpBenchmark to work manually

PALS is no longer automatically generating empirical benchmarks, so
this is part way through modifying empirical benchmark code to work
nicely manually in a controlled way.
Also moved plot line colour definition to be next to ChooseColours in
Utils.
Close netcdf files on errors
Fixed ORCHIDEE NEE read issue

ORCHIDEE NEE has dim (x,y,t,vegtype) where NEE values are already
weighted by vegtype fraction, and so need to be summed. Trivial comment
changes in files other than GetModelOutput.R
move ORCHIDEE munging to correct place