See #416

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

Year in header is here updated to 2017

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

To make the layout more consistent, I made new files:
Config.inc
ConfigInstall.inc
that are generated with a script, whereas:
Config.cpp
ConfigInstall.cpp
are included in the repository.
In this manner all cpp files are included in the repository.

Almost is not anymore supported in v2.3

This makes these options consistent with others.

THIS REQUIRES ./configure AGAIN!!

Now configure properly takes into account paths such as
--bindir=/path
etc

This implementation hardcodes all the path into the
src/config/ConfigInstall.cpp file. I followed the instructions on autoconf
documentation so that the paths can be changed at install time using e.g.

make install prefix=/path bindir=/path/binxx

This should be the standard behavior.

I removed the possibility to use PLUMED_SUFFIX and PLUMED_LIBPREFIX
since it was a bit too difficult to maintain.

I significantly simplified the src/lib/Makefile by using
the standard directory names for autoconf.

as an enviroment variable. This should allow to move
more easily a static executable of plumed.

I have implemented solutions 2 and 4 of #129

this close #129

This allows to conditionally execute regtests

The only way to have something working has been to include a "VERSION"
file in the root dir which should be updated by hand when releasing.
Additionally, plumed --git-version can be used

plumed info --version
returns the branch name (or something such as v2.0 in releases)

plumed info --long-version
returns a longer description (or something such as v2.0.2 in releases)

Also updated the src/release script accordingly

Files with gz extension are transparently compressed and decompressed.

Closes #17

This allows them to be automatically skipped when molfile has
not been linked

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

Added more ways to check if tools are installed. Now also
plumed --has-matheval
is allowed

Now the file containing the configuration options is a .cpp file.
This limits the effect of the change in the configuration to
a single object file and remove the need for BUILDAFTER variable
in Makefiles

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