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