installation: fix autotools rsync instructions

* Amends upgrade instructions (rsync in RELEASE-NOTES) in order to use
  new invenio-autotools.conf file created during upgrade.  (Keeping old
  file would mean not updating Invenio version number in the page footer,
  not taking into account possibly newly installed prerequisites, etc.)

Signed-off-by: Tibor Simko <tibor.simko@cern.ch>