I fixed the usage of stopflag in driver so that it is clearer
that the program stops at the end of the present step and not
at the beginning of the following. This is obviously equivalent,
but shows that scope of the flag can be reduced to be defined
at the inner of the MD loop.

Even if this is not a bux fix, I consider it as paired with fix #47
and I merge it to v2.0

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

I adapted the debug replica exchange stuff. Since running on multiple
trajectory could be useful, I leave --multi as a non-hidden option.

I slightly changed behavior of the hidden flag --debug-grex (now one sets the exchange stride, not the number of replicas - the latter is set with --multi). Thus, a couple of retests had to be updated

There was a bug when reading cubic cells

(Pointed out by Sergio Decherchi)

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

I used cppcheck --enable=all.

Namespaces are used now in bias/colvar/function/cltools

I added a src/cltools/CLTool.h which can be directly included from sources
in the cltools directory

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

With "plumed driver" it is possible to override the box in the trajectory
file using a --box flag. Works for orthorhombic or generic cells.
I also modified a regtest to that it checks this flag.

(adapted from Toni Giorgino).

Pdb was stupidly re-read at every step. Now it is only read at the beginning.

There is a new option "--pdb" which allows specifying a pdb file.

(adapted from Toni Giorgino)

This can be done with a command line flag
"--length-units XX" where XX is either a string (e.g. A, nm, …) or a
conversion number from nm (e.g. A is equivalent to 0.1)

re-passed in to main of CLTools.  Also fixed some mistakes
in the developer documentation for Colvars and Functions

command line tools easy to document in the same manner as Actions are
easy to document

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.

I added to driver the possibility of mimicking a
decomposition of the particle among processors with
a sequential criterion (similar to the gromacs
particle decomposition). Just use --debug-pd option.
Number of particle per processor is changed randomly
along the calculation.

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

I added an option --debug-float which turns the driver into
a single precision version to test interfacing with plumed.
Notice that it makes sense only for debugging.

I modified the command line tools stuff so that it is now possible
to access it using the Plumed.h interface (i.e. cmd(...)). This
allows to call the command line tools directly from other languages,
and is more consistent with the way plumed library is accessed from
MD codes. Notice that now also a plumed-runtime executable
is produced, which looks for PLUMED_KERNEL variable at runtime
to choose the proper library to load. Since all the command line
tools are built inside the library, this just means that a
different plumed version is used (similar to runtime mode
for patching MD codes).

Moreover, I hard-coded the PLUMED_ROOT variable in the
PlumedConfig.h header file. In this manner, it is sufficient to
have plumed in the path.