Here you can use regex to refer to argument in a list
For example in
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
d1: DISTANCE ATOMS=7,17 COMPONENTS
PRINT ARG=(d1.[xy]|t[0-9]) STRIDE=100 FILE=colvar FMT=%8.4f

Currently the .diff file is compulsory, the .config is not. So, the list
of MD codes should be built looking at .diff files

This is the standard path for linux distribution. Thus "make install"
will fail unless run with root permission or unless PLUMED_PREFIX is
explicitly set. I also fixed DYLIB path for mac (plumed path
should be prepended)

Fixes #7

to reflect the implementatin of INTERVAL and ALPHABETA

Now, for consistency, the time units of SIGMA in METAD for the
ADAPTIVE=DIFF scheme is in timesteps to be consistent with the rest of
the program. Documentation, printout and regtests are done.

(suggested by candrewn@gmail.com)

It was wasting space (especially the developer one) and anyway improperly
formatted. Could be readded later if we fix formatting.

For some reason on my local linux machine doxygen does not
replace the variables $extrastylesheet and $relpath in the
PlumedUserHeader.html file.  As we are not using these variables
I deleted them from the header files.  I think this will cause problems
if we ever choose to use a custom css file for the documentation or if
we use the CREATE_SUBDIRS option.  I cannot imagine that we will ever
use these options but I thought I would mention these problems in the
log.

I added a directory CHANGES where we can add short description
of changes among versions. I use a separate file for each branch
(v2.0.txt now, then we can add v2.1.txt in the master branch)
so that it will allow merging from old branches to new branches
as usual.

ATOMS=1,4,7,10
can be replaced with
ATOMS=1-10:3

(suggested by Paolo Raieri)

Webpage with modules is not generated if no modules have been installed

Two users have complained to me that the manual is rubbish.  I subsequently
found out that they had built the manual without first building the code. So
they didn't have any of the keyword descriptions in the manual that compiled
This manul now can't be compiled if the code isn't compiled.  It seems that
having lots of error messages generated when the manual compiles wrongly is
not sufficient for some people!

This funcitonality allows you to add tutorials written in Doxygen
and links to external websites.  They are called How Tos though

An output file was not set

This allows proper documentation to be written.

I added a regtest for INCLUDE but not one for LOAD,
as dynamic loading could not be available

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