This is a huge commit, applying indentation to the whole
code.

See #215

Given header file.h, it is good practice to have a file file.cpp
that includes it as first header.

I just fix the order of includes here. There are still several
headers which do not have a corresponding cpp file, and also
a few that are not included anywhere (which is obviosuly an error).

I will fix them in a later commit.

Prvented division by zero in calculation of average field and added TRANSFORM analogues of multicolvar filters

Changed from left to right handed axis system in MultiColvarDens and now doing proper spatial average of multicolvar values

N.B. Change to ActionPilot.h just makes getStride a public
rather than protected method.

Now there is an option to update grids only in the region around where
the contour was found in FindContour