Precise:

cd ee
tar cfj footprints.tar.bz2 \
  ` git ls-files '*.mod' '*.kicad_mod'
   git ls-files '*.fpd' | sed 's/\.fpd/.mod/'
   cd hw/kicad-libs
   git ls-files '*.fpd' | sed 's|^|hw/kicad-libs/|;s/\.fpd/.mod/'`


# ignore the warning about hw/kicad-libs/modules/qfp-gen.mod

Simple:

cd ee
tar cfj footprints.tar.bz2 hw/*.mod hw/*/*mod hw/kicad-libs/*/*.mod