Added a routine to ActionVolume that I need to make Cavity (hidden feature) work
Removed the need to explicitly state "make lib-static"

On machine without dynamic libraries, just leave "SOEXT"
undefined in the Makefile.conf. Compilation of dynamic libraries
will be skipped.

I also fixed the src/lib/Makefile such that I am sure that no .so
object is generated for machines where SOEXT is undefined
Merge branch 'master' of git.assembla.com:plumed2
Fixed Makefile

Something wrong could happen to inc files depending on the order in which they are produced
keywords now tells you what keyword was duplicated when you make a mistake
Fixes to neighbor lists in ActionWithVessel

ActionWithVessel is calculating sums.  For many of the quantities
ActionWithVessl calculates (e.g. less_than, more_than, coordination numbers )
each of the terms in the sum is a number between zero and one. A reasonable
way to implement the neighbor list is to ignore terms less than
a small number (TOL) at every step.  On neighbor list update steps we recalculate
all the contributions to the sums.  Anything less than NL_TOL (a number less
than TOL) can safely be ignored until the next neighbor list update step.
For complex variables (e.g. q6) a considerable speedup can be acchieved just by
setting the value of TOL.  However, for variables such as coordinationnumbers,
where calculating all the distances is the most expensive part of the calculation,
the neighbor list and a TOL value are required to get the code to run fast
Added manyrestraints module

At the moment this can only be used to place a wall around a cluster
so that the atoms stay within a bubble centred on the centre of mass
Made SPECIESA, SPECIESB work when there are aroms from SPECIESA duplicated in SPECIESB
Made multicolvar and MultiColvarFunction inherit from a common base class

This makes these two classes slightly simpler.  It also allows one to
use MultiColvarFunctions on MultiColvarFunctions.  We can thus do things
like the value of the dot product of the q4 vector on a atom with the
q4 vectors on the atoms in the first coordination sphere averaged over a
subregion of the simulation box.
Updated documentation
Fixed manyrestraints

Some files that are automatically generated were mistakenly added to git repository
Fixed embarassingly stupid bug in ManyRestratintsBase.
Moved secondary structure variables out of multicolvar

Now all multicolvars can have a central atom position and can be used in
multicolvar functions.  This makes the code a bit clearer.  Also secondarystructure
variables are now faster as much copying of derivatives is removed.
Fix in DUMPATOMS

File was open in a manner that do not provide autobck
Bug fix

ENDPLUMED was not correctly understood
Added possibility to retrieve more info from MOLINFO
Added small tool to detect file extension
DUMPATOMS can print gro files.

If MOLINFO are available they are used in the resulting gro file.
Filetype is detected automatically, but can be enforced.
Atomnames are also written in xyz files.
Added regtest for DUMPATOMS
Added tool to convert string to float single precision