Similarly to what happens in Colvar class, I made
also for ActionWithVirtualAtom a method setBoxDerivativesNoPbc
that can be used to set the virial contribution when the Pbc have not
been used in the calculation of derivatives.

This should make the addition of new vatom actions easier

I implemented a framework to provide the virial corrections for
virtual atoms that are non-linear functions

Addresses #74 (warning only)

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

If you want to but a plumed_assert in a loop you should now use
plumed_dbg_assert / plumed_dbg_massert.  This will not be included
in the code if you compile with -DNDEBUG

Class providing actions should have the same name as the input directive

All the source code have been moved into subdirectories of src/
Some of these subdirectories are treated in a special manner:
src/wrapper contains the wrappers for MD codes
src/main contains the main.cpp file
src/config contains files generated without compilation,
  just based on configuration info
src/lib is the place where executables and libraries are put
  at the end
src/cltools contains the command line tools
src/tools contains plumed tools (reusable classes)
src/basic contains PlumedMain, Action hierarchy and other basic stuff
src/multicolvar contains MultiColvar stuff
src/imd is the interactive MD (still not totally portable).

Notice that, to allow easy inclusion of .h files from other modules,
I link all the directories in src/ into module directory. In this
way it is possible e.g. to write #include "config/PlumedConfig.h"

See src/README and src/basic/Makefile to understand how inter-module
dependencies are set

Fixed derivatives for Ghost Atoms. At least I hope so. Is there a way to to numerical derivatives of ghost atoms?
If not, we need it!!! Max

as suggested by Gareth

I added a PEOPLE file containing list of authors and a script
(src/header.sh) which applies the Licence to all the source files.

It can be applies multiple times (it automatically deletes the present header
and replace it with the new one). Thus, to change the header, edit header.sh
and execute it.

The computed ghost atom is stored as a virtual atom that can be accessed in
an atom list through the the label for the GHOST action that creates it.