I think this is more coherent with other cmd() calls.

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

cmd("useNaturalUnits") was erroneously crashing

Still we should write some doc. Also, there is not regtest for this...

I moved the reference together with the others (using cite()) so that
it is more visible. I also updated a bit the description

uninitialized variable (from last commit)

(suggested by Paolo Raiteri)

ENDPLUMED was not correctly understood

Can be activated with DEBUG DETAILED_TIMERS, and provide action by action
timing. Useful for optimization

Gromacs patch has been fixed (this is compulsory for big Endian machine)

Energy was not calculated at every step. Now, gromacs ask to plumed
whether energy is needed at that step and calculate it accordingly.

I also updated the patch to 4.6.1

When the log file is chosen by name (cmd("setLogFile"...))
there was a problem due to an apparent double initialization
of log file. Now, logfile is open when cmd("setLogFile"...)
and, in case it is still not open when cmd("init") is called,
it is opened to stdout

This I found to be helful when debugging on the cluster with buffered output.

When using IFile or OFile only, it is sufficient to include
one of the two header files.

Also, consistently:
PlumedIFile -> IFile
PlumedOFile -> OFile
PlumedFileBase -> FileBase

I replaced all the "using namespace PLMD" statements with explicit
namespace PLMD{ …… }. This is more clear and simplify the syntax for
defining operators

Now the file containing the configuration options is a .cpp file.
This limits the effect of the change in the configuration to
a single object file and remove the need for BUILDAFTER variable
in Makefiles

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

In the end it is just an aesthetic point, but I think it allows
to document the action in the proper place

Using a RESTART keyword in the input, files are automatically
appended. When not used, files are backed up (a la gromacs).

Notice that this works only when using open("file"). The rationale
is that if you say open("file","a") or open("file","w") then you
know what you are doing. I also removed the extra mode specifier
for PlumedIFile (it was redundant: always "r").

If the behavior is not clear enough we can change it...

PlumedFile's were not flushed correctly

While trying to use the new printField stuff for metadynamics I
realized that it is simpler if one does not need to explicitly
declare which fields will be printed.

I also fixed the formats in two regtests

Documentation is still a bit poor. I used it to replace
the Log implementation and also for in the GenericPrint class.
In the log, this implies a small change (FIELDS line is
written in also in the log).

I tried to make everything so that regtests are not affected. Only,
change, now the rt17 (using _ROTATE) works correctly, writing
field names as they are updated.

of setting the seed from the plumed.dat files. iy=0 in Random.cpp

as suggested by Gareth