I think this fixes #143

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fix a problem when md.log was appended
plumed was trying to write on it after
md.log was already closed

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@alexvoronov pointed out that the example was actually wrong.

same as b2b2176c

Fixes #140

I checked that this regtest fails without last commit

Related to #190

No EOL at the end of the file is only tolerated in input file
(e.g. plumed.dat) and not in other files (including HILLS files).

Indeed, when using multiple walkers, it is possible that transiently
the HILLS file from other walkers have incomplete lines.
With this fix, those lines are ignored and read at the next iteration.

This fixes #190

When doxygen is not found, doc is disabled

Pdf manual takes a lot of time to be compiled.
Since it is not very useful, I disable it by default.

Notice that on travis CI it is enables during configure.

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notice of 30734458

With this change it looks I can solve an issue on my workstation
that has been reported on the mailing list (multiple linking
of Plumed.o object)

some files where not up to date

Gaussian kernel functions were normalised incorrectly.  This should
only cause a multiplicative scaling of the histograms calculated
using the HISTOGRAM action

This reverts commit dcd4a63d.

This reverts commit 3758d552.

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