Changed installation layout for objects

Instead of replicating the whole tree upon install,
now objects are copied to prefix/lib/plumed/obj
and assigned a number.

When possible, objects are grouped in a single kernel.o
with ld -r (tested in configure). This saves a lot
of disk space.

I also removed from the install directory some other
useless files.

The Plumed.inc/cmake files when installing
are generated in a different way from the ones
used prior to installation. Thus, to avoid too many
repetitions, I wrote a small awk script the transforms
Plumed.inc to Plumed.make