Ready for merge. Nothing should change with existing Makefile.conf.

To be consistent with the paper, plumed is always capital letters.
I also changed 2.0 -> 2 and 1.0 -> 1 for sake of generality

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)

Fixes #7

the parts that are contained in the code

I also upgraded the doxygen configuration files to 1.7.4 version