Given header file.h, it is good practice to have a file file.cpp
that includes it as first header.

I just fix the order of includes here. There are still several
headers which do not have a corresponding cpp file, and also
a few that are not included anywhere (which is obviosuly an error).

I will fix them in a later commit.

style warnings

I removed the NOPBC key from manual (it is not used)

[makedoc]

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

I replaced everywhere it made sense the new Communicator class
syntax. This commit is not strictly necessary, but provides
examples of the simpler syntax so I think should be merged

Now the stride for the neighbor lists in the path implementation
are in timesteps. By now this means that PATHMSD and PROPERTYMAP are
defined with e.g. NEIGH_STRIDE=5

Now the code crashes in the following cases:
1. An exchange is attempted on a step where neighbor list for COORDINATION
(or DHENERGY) are not updated
2. An exchange is attempted and neighbor list for PATHMSD or PROPERTYMAP are enabled.

The second should be fixed better to allow using strides for lists which are
divisor of the stride between steps. The better thing will likely come later, at least
the code is safe now.

Mostly unused variables

I used cppcheck --enable=all.

Allow to better isolate the heavy part to be parallelized

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

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

Detected with -pedantic

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.

This clarifies a bit the developer doc

one liner and has Spiwok isomap inside