Fix build of share/template when installed

It is now possible to build the analysis tool template using the
Makefile.pkg and the CMakeLists.txt that are installed with it, at least
under some conditions.  FindGROMACS.cmake could probably be improved
further by using gromacs/version.h to detect the version for those
installations where it is present (4.6 and up); the current list of
functions is confusing (init_domdec_vsites, for example, already appears
in 4.6, but causes the detected version to be set to 5.0), and requires
extra maintenance for each release.

Remove obsolete Template.mak, which was used by autoconf to generate an
installed Makefile.

Change-Id: Ibcaa792b721db7fc9729710e36ace29bddbb82c3