the header files for these abstract base classes

you an error as <label> is not a valid html tag

Doxygen groups

I think this could allow us eliminating the DEVELDOC
preprocessor.

The "before" vector was private and not used anywhere. Now it is only
possible to know on which Actions this Action depends and not
the opposite (which Actions are dependent on this).

to do with assembla

Now the FILE descriptors in and out are properly used

Conversion is done with trivial int operations, avoiding sprintf() and sscanf()

switching functions for the various contacts. Also made the output prettier.

you try to do this.

fields and the various functions of the distribution of whatever the collective
variables are

the WITHIN keyword range as well as the number of colvars within a given range.

The point in CV space can be specified using a pdb file, hence the changes
to Action, Value, etc - all these changes are all so that you can calculate CVs from a
pdb input file.  Whilst I was messing about I noticed a potential problem with
natural units and input pdb files.  As we are in natural units there is no
way of knowing how to convert the pdb from angstroms (unit in pdb)
to the natural length unit.  For these reasons I assume that when one is in
natural units pdb input files are also in natural units, this required changes
in ColvarRMSD and my new ColvarTarget routine as well as a small change in Atom.h.

Added funcitonality so that one can restart field cv calculations
Added field cvs for contact maps

I tried to remove a lot of includes using forward
declarations

Changed the name of the method which sets to zero the
elements of a Vector or Tensor. The name clear() was
ambiguous as for STL containers the clear() method
also deallocates data.

Now it is possible to spread a single, long 
option on multiple line using parenthesis. E.g.
group: …
GROUP ATOMS=(
  10 20 30 50-100
  110 200
  )
…
Notice however that one still needs to use triple dot
to mark continued lines.

Due to default values in flag, it makes no sense to have
a flag with default value "true". I thus removed PBC from
the keywords for colvars. Now they are default on and can only be
switched off (with NOPBC).

Another out-of-array bug. This is tricky: if an array
could be empty, do not use &buffer[0] as it might
trigger an out-of-bound error.

It was triggering the boundary checking (fortunately on linux
-D_GLIBCXX_DEBUG works!).