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

Avoid warnings and increase portability

CENTER creates an atom as a weighted average of other atoms.

Periodicities of values are stored as strings inside Values.
These strings are output as constant fields inside the colvar and
hills files.  In addition the fact that we now use strings means that
when you have a function and you have to specify its periodicity you can
use PERIOD=-1.5pi,1.5pi or some other thing like that

These two very simple actions need to retrieve the time as a
quantity to be used wherever you want (in my case in
matheval) and BIASVALUE needs to put a bias on a value you
create (for example a bias can be created with matheval)

is not calculating a volume

Copy constructor and assignment operator are now disabled
to allow erroneous usage e.g. in STL

This is a very big commit on the master branch. The way plumed write files (such as COLVAR/HILLS /etc) has been completely changed. We now have:
* automatic tagging of the columns with an initial "#!FIELD" line
* automatic backup when trying to overwrite files (a la gromacs)
* restart is driven by a standalone line "RESTART" in the input file, which activate restart for all the other keywords.
This may affect quite a bit the behavior of plumed. A few examples:
* If you use metadynamics, HILLS format is slightly changed (there are tags now). Have a look at one of the newly produced HILLS file
* COLVAR files are not anymore appended by default: you have to specify RESTART (on a separate line)
* unpredicted bugs may have been introduced!

Detected with -pedantic

Removed unnecessary include and added bibliography

PATHMSD -> FUNCPATHMSD
CVPATHMSD -> PATHMSD
ISOMAP is an alias for CVPATHMSD

This shows the ISOMAP as a different flag even if it share the same
implementation with the path. For now, also the keywords are identical,
this certainly has to be fixed.

Keeping merging-plumed-file-tool branch up to date

This clarifies a bit the developer doc

In this way the used will be forbidden to use vector<Plumed> (which would not indeed work)

Now all of these classes either allow copy constructor/assignment
or forbid it. This allows either to use them in STL vector,
or give explicit compilation errors if it is not safe to do it.

local classes were declared in PLMD namespace. Now they are local to
FunctionPathMSD class

I merged again from the master branch to keep it in sync.
There were a few conflicts which I solved in the latest
Gareth's stuff to fix units in DUMPATOMS.

Conflicts:
	src/GenericDumpAtoms.cpp

one liner and has Spiwok isomap inside