One can now produce a Makefile.conf and a sourceme.sh
using autoconf. Just type:

./configure

Or maybe

./configure CXX=icpc

In case you want to use mpi, just use:

./configure CXX=mpic++

Everything should be smooth. I took care that the generated Makefile.conf
is compatible with those stored in configurations/. In this way,
one can always resort to a saved configuration file. Moreover,
jumping between git branches (without need of reconfiguring) will be
easier.

More info on the manual page (no need to use autoconf to compile
the manual and see that page)

Closes #46

It is now possible to install plumed with "make install".

Installation is done just copying most files (e.g. obj needed
for patching) and fixing hardcoded paths. The advantage is
that it is possible to fix a location with environment variables
PLUMED_PREFIX (e.g. /opt/local/) and a suffix with
PLUMED_LIBPREFIX (e.g. 2.0.0). This will help in installing multiple
plumed versions in the same path.

Moreover, also include files are copied to e.g.
/opt/local/include/plumed, so that it is possible to use the plumed
tools library as a normal system library

There was a problem if starting compilation in some directory.
Now also the links to other directories are generated recursively,
thus are by construction up to date for all the used modules.

Notice that config/ and wrapper/ are treated as special cases

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