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