Couple of fixes to 'plumed mklib'

(cherry picked from commit 2ccba594d5839167ec4e3f570b8c63f5a61b8d3c)

    Backported changes from master to fix "plumed mklib"

    There was a problem with Makefile.conf as produced with ./configure
    if used in v2.0. This fix allows to use new Makefile.conf with old
    (2.0) plumed.

    This should fix the problem with rt15 mentioned by Gareth in
    the discussion of #76

Conflicts:
	src/config/Makefile