hopefully will avoid some mail to the mailing list

close #124

Allows to avoid verbose logging. The option is now used in user-doc/extract
to simplify the generation of code-specific notes

(cherry picked from commit 7152d46f)

Conflicts:
	patches/patch.sh

This allows one to create information on the differences in
the various patching procedures by executing:

plumed patch -i

This information is also put into the online manual

(cherry picked from commit a273bb84)

Allows to avoid verbose logging. The option is now used in user-doc/extract
to simplify the generation of code-specific notes

This allows one to create information on the differences in
the various patching procedures by executing:

plumed patch -i

This information is also put into the online manual

I added a new mode to store patches. If one saves them with
--save-originals (instead of -s) what happens is that
/patches/codename.diff
will be a directory. Instead of storing diff files there,
we will store original/modified pairs.

When patching, if a directory is found in
/patches/codename.diff
the diff are computed and then reapplied on the actual files.

The only change is that the diff is not stored but re-computed on-the-fly.
This has a completely equivalent effect of the original way.
E.g., one can patch two slightly different versions
of an MD code with the same patch.

However, it has the advantage that stored files are more friendly.
E.g., one could directly edit them. Also the git-merge of two
different patches should work better now.

It is more flexible since it allows adding new files instead of just patching

An MD engine could have no patch, and do everything with scripting

Avoid clashes between same patch created by different people

- the patch.sh and src/lib/Makefile are the same of those in the branch tmp-cmake

the CMAKE patch works different from the former gromacs patches:

- untar gromacs-4.6b3 (./gromacs-4.6/)
- in gromacs-4.6/ copy patch.sh and patch
- mkdir a build folder ./gromacs-4.6/gmx-plumed/
- in gmx-plumed/ run cmake ../ to configure gromacs
- make / make install as usual

there is a bug somewhere for which a "-l" is added before
Accelerate in "-framework Accelerate" thus resulting in a
compilation error.

there was a wrong path

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

This is to allow arbitrary scripts to be executed while patching.
Note that one should also define an equivalent function for reverting.
USE WITH CARE!! And let's try to be strict with this so that patch -r
will be usable for all the codes.

Modified the "plumed" script so as to simplify the addition of new
tools. To add a new tool just put a script in tools/scripts with extension
.sh. The script should understand the keyword "--description" which is used
to build a summary of available scripts in the main "plumed" script.

This is the draft version that I prepared and that we will use as
a starting point. Still it is a bit dirty, and I will try to improve
documentation and delete unused routines