Starting interface to NetCDF C API
Updating NetCDF C API

C API stable, compared to C++ API
Fixed include ordering for Tornado

Complains if anything is included before mpi.h

Signed-off-by: Ben Dudson <bd512@york.ac.uk>
Added averageX function to mesh and smoothing.hxx

Averages Field2D and Field3D variables over the X dimension
Added Python utilities (calculus, spectrogram)

o calculus.deriv2D   - 2D gradient using convolution

o calculus.simpson_integrate    - Integrate 2D data using convolution

o spectrogram.spectrogram  - Creates spectrograms using the Gabor transform
Merging changes from Jarrod

o averageX function
o Python routines
User manual: Added small section on restarting runs
Small updates to Python collect and test routine

Making code more robust to missing data.
NetCDF C API code seems to work

Passes all basic tests, but still need to run drift and interchange
tests (laptop too weedy...)
Modified configure script to look for NetCDF C API

This API has remained quite stable across multiple versions
of NetCDF, whereas the C++ API has been changed significantly.
This code should therefore work on more systems.

The API used can be specified using an additional flag

--with-netcdfapi=c    Use the new C API (the default)
--with-netcdfapi=cxx  Use the older C++ API
Merging new NetCDF interface

Makes the C API the default, so should be thoroughly tested
before being merged into master