Changes to the code are there so that I can reference the atoms
page in the descriptions of keywords that read atom numbers.  I also
changed the input to multicolvar functions.  I stopped using the ARG
keyword in these actions and used DATA instead because you are refering
to the data calculated in a multicolvar as opposed to a scalar quantity
calculated by a particular action.

- added regex in Misc
- added BIBLIOGRAPHY in the top bar

there where random "@" appearing here and there. Fixed now

"extract" is way faster. Additionally, spaces are better preserved
in the manual (especially in indented input files)

@giovannibussi, which error did you get?

1) default output file is histo.dat
2) --idw with --histo now select a subset of fields and ignore all the others
the only missing feature at the moment is that it still do a free energy
instead of a probability density because I have to add the calculation of
the normalisation.

list of PP files is now generated automatically

autoconf was giving me errors. Since we are not using it anywhere,
I temporarily comment this out

- When using GRID and ADAPTIVE one must use SIGMA_MIN
- GRID BINNING is now automated also in the case of adaptive gaussians
- if GRID MESH is > 0.5 sigma there is a warning in the log (we should think
of making this an error, but that will break two regtests, what do you
think?)

Now the "nerd" part (stack trace) is dumped first, and is surrounded
by ***

The Doxyfile was appended instead of being replaced at any
new generation of the doc