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

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 "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).

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.

Prefix operator preferred to postfix operators with
non-int types
(as suggested by cppcheck)

Many checks on size() transformed in checks on empty()
(suggested by cppcheck)

Many arguments are now passed by reference
(suggested by cppcheck)

was for an older version of the way I implemented numerical derivatives
and is now not strictly necessary.  I don't fully understand why it
was causing problems though.  It is a bit strange as the same check
worked (for the same action) elsewhere.

is an overlap integral between the current field and some reference
field ( this can be a sum of fields visited at previous times ala metadynamics ).
To test the derivatives of the field I changed calculateNumericalDerivatives
this routine can now be passed an ActionWithValue so that you can differentiate
objects where something other than a value is passed between Actions.  Currently
only histogram style field cvs are implemented.
Wrote documentation for FIELD keyword and for MOMENT keyword.  Also
rethought numbered keywords and so changed the keywords class a little bit
Changed number of decimal places in tests so that they worked on other
computers.  Also made test 23 much less expensive
Fixed a very persisent bug in field cvs - horay!!!

Added regtests for histogram and within stuff
Added regtests for MULTICOLVAR and for neighbour list in MultiColvar
actions

Fixed other places in action where one would get similar errors
to what was observed for LABEL in GenericFlush and Units.

various actions below.

some of the English and in some cases writing new documentation.  Also sorted
a number of issues that arise because of the awkward formatting that is
Doxygen requires

Added keyword registering functions to Action, ActionWithValue, ActionWithArguments and ActionSetup.
Also added variables so that the keyword list can be passed to the Actions

(merged from gat2-reorder branch)

Added keyword registering to all the action classes listed below

(merged from gat2-reorder branch)

Added register keywords functions to all the classes below
(merged from gat2-reorder branch)

Fixed the registerKeywords routines in the committed subroutines

Made sure colvar is adding keywords for numerical derivatives

Oops... genericDebug should register keywords for action pilot.  It does now

Added keyword registering for moving restraint

Added keyword registering for NATURAL keyword

COMPONENTS should have been registered as a flag and not an optional oops

Basically I replaced all objects included in other objects with references, so as
to eliminate the need to include the corresponding header file. In this manner the
entanglement of compilation is greatly reduced.
Forward class declaration is now used everywhere excepted for:
* cases where it is impossible due to inline functions
  (for efficiency or because they are templates)
* cases where it is impossible due to inheritance
* small objects of fixed size such as Vector/Tensor/AtomNumber/Units/Pbc
* classes of std:: namespace (it is not possible to forward-declare them).

I replaced many of the "low level" assertions, trying to add messages here and there.
Still, this is mostly for developers: errors in the input file should get better reports.

Now it assumes that a file is open for writing when char
"a" "w" or "+" are used in fopen mode.

Similarly to plumed1, fopen on nodes different from the first opens
/dev/null file. Notice that this is done only for writing (so as
to allow non-root nodes to read files). Also, it is done only for
fopen called inside Action, using the Action communicator. This should
allow parallelization over CVs (setting a different communicator for each
of them).

I moved the tools to open a file with a specific prefix to PlumedMain.
This allows easily to use them also to open the input file, which in
turn means that we will be able to do bias-exchange and Hamiltonian
replica exchange

It is now possible to automatically add a suffix to
all the files opened through the Action::fopen tool.
Opening is done as follows:
First the file+suffix is tried.
In case of error the file without suffix is tried.

In this manner, it should be possible to provide a single
input file also for replica exchange stuff. For output files,
it should make any difference.

I also added a stupid keyword to test this feature. Just use
_SET_SUFFIX pippo
in the plumed.dat file to add a suffix pippo to opened files

This is to be sure that requestArguments() and requestAtoms()
are only called from the right place, i.e. prepare()
or initialization

There is a generic ActionWithVirtualAtom class which can be used
as the base for Actions able to add new virtual atoms to the
system. Virtual atoms are stored in Atoms, can be referred to using
the label of the generating action. Automatically, they are
assigned an AtomNumber which exceed the real atom numbers
(e.g. if you have 108 real atoms, virtual atoms will have
indexes 108,109,...). They are automatically understood by
the parser provided one uses the parseAtomList() function.
Each instance of this class only generate a single virtual atom.
The nice thing is that, since lists of atoms can be dynamically changed
(e.g. by neighbor lists), dependencies are handled properly
and a virtual atom is only computed of the steps on which it is needed.

I also implemented a practical case, which is center-of-mass
(GenericCOM).

New virtual method for Actions which is called at steps when action is
active just before atoms sharing. This is the right place where Actions
can change their atom requirements. E.g., you can do

class ColvarSomething{
...
void prepare();
}

void ColvarSomething::prepare(){
// take here your decision and eventually change the requested atoms
}

To retrieve the timestep and to retrieve the periodicity

I overloaded fopen and fclose inside an Action in such a manner
that a list of open files is kept. This allows to flush them implicitely,
without requiring people to write an explicit flush() method.

Implementation is rather general and allows one to use them not only for debugging but also for real calculation. A keyword NUMERICAL_DERIVATIVES can be used in directives such as COLVARs or FUNCTIONs, and automatically performs numerical derivatives instead of analytical ones. Moreover, I added a DUMPDERIVATIVES directive which prints on a file the derivatives of the (ARG) colvars. E.g.:
DISTANCE LABEL=C1 ATOMS=0,1 COMPONENTS
DISTANCE LABEL=C1n ATOMS=0,1 COMPONENTS NUMERICAL_DERIVATIVES
DUMPDERIVATIVES ARG=C1,C1n FILE=derivC1
will define two CVs, with the same value, but one with analytical and the other with numerical derivatives, and will write two columns on file "derivC1" with the derivatives, which can be compared for debugging.

BE CAREFUL: I did not test it with non-orthorombic cells, there may be problems in the virial components