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.

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