Changed default install path to /usr/local

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)
Changed reference to plumed 1 paper

I moved the reference together with the others (using cite()) so that
it is more visible. I also updated a bit the description