Adding bout-config script

Intention is to make it easier to use BOUT++ as a library
and to use multiple versions e.g. through Modules
output.make to capture flags for use in bout-config script

Flags needed to compile e.g. PETSc are available at configure
time. If the environment changes later then PETSC_DIR etc. may
change, in which case the link flags could be different.
Added example makefile to use bout-config script
Merge branch 'runscripts' into next