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.

[makedoc]

I cleaned up some of the (innocuous) warnings

The original implementation I did of this was numerically unstable because
a minimisation rather than a root finding algorithm was being used.  In this
new implementation I have also changed it so that you can specify an upper
and lower bound in your search for a surface

Also made it so that you can change the origin in
DumpMultiColvar and also fixed a bug in MultiColvarDensity

Related to: e1b845b4

Now the type is defined with a typedef so that it is easier to change it.

I also set the type to size_t instead of unsigned long long.
This should be more portable.

This only works for three dimensional grids

(cherry picked from commit ab739533)

grids are quite faster in this way, and I think that all the asserts
were redoundant with those in the initialisation.

- accumulate standard histogram without using kernels
- accumulate frequency instead of normalised probabilties
- convert the histogram to a free energy

The fix to #39 was incorrect since adding an int to a string
does not print it.

I also removed the redundant check that index is positive (it is unsigned)

I removed an assert and added an if then plumed_merror

close #39

I removed an assert and added an if then plumed_merror

close #39

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

I think the way pbc were applied was not correct (Fix #19).

now the cltool for sum_hills takes the --fmt keyword to specify the output format
and add small mods for parallel support (not yet available)

An assertion is triggered when asking for values/derivatives outside
the domain