@tetsuyamorishita I merged all your commits into a single one.

Notice that I reimplemented the Communicator function that you needed
(Max) together with a few others (Min and Prod).

See #422

The source code from crystallization allows you to calculate
Q4 and Q6 parameters.  You can also calculate local Q4 and local
Q6 parameters and you create compound collective variables based
on the relative orientations of internal vectors in adjacent molecules.

Regtests for this functionality are reasonably thorough.  Manual is
not so great as yet

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