Especially when printing size_t it is better to use << operator
which always uses the right size.

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

Also tidied up how STRIDE and USE_ALL_DATA works for analysis
objects.  Now everything works in a manner similar to GRID

You can now use COLLECT_FRAMES to collect pdb data from the trajectory
and output a pdb file that contains the underlying atomic coordinates
in pdb format even if you are not using the rmsd distance to measure
the dissimilarity matrix for dimensionality reduction.  Also fixed
a number of bugs.

To do this I had to make requestArguments in ActionWithArguments
a const method is this a problem?

The reference module means that you can use different types of metric when
calculating the separation between the instantaneous position and a reference
configuration.

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

clang -Wextra-semi

The guard "ifndef/define" has been updated so as to also include the
module name. This is important as it will allow files with the same name
to be used in different directories. Modification was done automatically
using header.sh - just run it routinely to keep names consistent

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

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.

The point in CV space can be specified using a pdb file, hence the changes
to Action, Value, etc - all these changes are all so that you can calculate CVs from a
pdb input file.  Whilst I was messing about I noticed a potential problem with
natural units and input pdb files.  As we are in natural units there is no
way of knowing how to convert the pdb from angstroms (unit in pdb)
to the natural length unit.  For these reasons I assume that when one is in
natural units pdb input files are also in natural units, this required changes
in ColvarRMSD and my new ColvarTarget routine as well as a small change in Atom.h.