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

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)

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