Fixes #582

This commit contains changes automatically generated by plumedbot on Travis-ci.

close #263

After \par Examples there should be an empty line

[makedoc]

Notice that almost all files were updated with the astyle commit
2813d759

Year in header is here updated to 2017

I replaced
verbatim
endverbatim
with
plumedfile
endplumedfile

in (hopefully) all the places where it was appropriate.

This is a huge commit, applying indentation to the whole
code. Notice that this commit is made on master branch
after having merged with -s ours from branch v2.3

See #215

This is a huge commit, applying indentation to the whole
code.

See #215

I added the possibility to personalize charge and mass units
in the same way as length, energy, and time units were treated so far.

Notice that since two new cmd() strings have been added to set
units from an MD code, it is necessary to increase the API version
to 4.

I also added the appropriate developer documentation.

Fixes #179

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

Since the SetupMolInfo action is used by other ones, I left it
in core/. It is however registered in setup/, so that it can be excluded
disabling that module. Moreover, I added a method so as to remove
a friend statement in PlumedMain

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 will allow to parse units also in places different from SetupUnits.
I also modified the Units class in such a manner that data is private
and access is safer. This required to change all around accesses
to its components.

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.

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

Added keyword registering functions to Action, ActionWithValue, ActionWithArguments and ActionSetup.
Also added variables so that the keyword list can be passed to the Actions

(merged from gat2-reorder branch)

Added keyword registering to all the action classes listed below

(merged from gat2-reorder branch)

Added register keywords functions to all the classes below
(merged from gat2-reorder branch)

Fixed the registerKeywords routines in the committed subroutines

Made sure colvar is adding keywords for numerical derivatives

Oops... genericDebug should register keywords for action pilot.  It does now

Added keyword registering for moving restraint

Added keyword registering for NATURAL keyword

COMPONENTS should have been registered as a flag and not an optional oops

I tried to also add error messages, at least when I knew the meaning
of the assertion...