Made .gitignore ignore regtests and src directories modules that are shipped separately to the plumed core

Mac just works. Linux is case sensitive

This is useful if you have some functionality in a base class that
you want to remove in a derived class

This involved splitting the code for reading an argument list from the code
for interpretting it, adding a function for reading the ARG argument from the pdb and
interpretting things like ARG=d1.* to ActionWithArgument and adding a routine
to PDB which allows you to replace the old ARG=d1.* with the newly interpretted
ARG=d1.x,d1.y,d1.z

To get the forces on the vessels you now call getForcesOnVessels this returns
a bool which tells you if you need to call ActionAtomistic::setAtomicForces or
ActionWithArguments::addForcesToArguments.  Separately numerical derivatives
were a problem if you had an action that inherits from both ActionAtomistic
and ActionWithArguments.  This is now not a problem as you can, in a manner of
speaking, specify where the atomic derivatives start when you call
ActionAtomistic::calculateNumericalDerivativea (i.e. after the derivatives wrt
to the Arguments )

This is associated with the fix of VOLUME derivatives

They were not implemented. A separate colvar (CELL) is coming soon

Notice that now it is also possible to use VOLUME with NUMERICAL_DERIVATIVES
(so as to debug). I tested with NPT and a box of water and seems to work correctly.

(From Paolo Raiteri)

This bug only appears when you store information so for things like moments
and proper multicolvar functions as opposed to Region, which is a fake
multicolvar function

Thanks to Paolo Raiteri

Seems to work with a simple example.
Use with care: not very tested yet!

It is more flexible since it allows adding new files instead of just patching

An MD engine could have no patch, and do everything with scripting

Links to used modules are made automatically by Make. They should not be saved in
the git repository. I think I already fixed this, but maybe it was not properly
committed

I converted from xyz to gro a regtest where boxes of different
shapes were used. This is to verify that box reading (with --igro)
and writing (with DUMPATOMS) is consistent.

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.

ENDPLUMED was not correctly understood

File was open in a manner that do not provide autobck

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.

Some files that are automatically generated were mistakenly added to git repository

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.