`write_default_input_file` creates duplicate `*_species_<n>` namelists

[Peter Hill]

Running bin/write_default_input_file creates defaults.in with a couple of duplicated namelists:

$ grep species defaults.in
&dist_fn_species_knobs_0
&dist_fn_species_knobs_0
&species_knobs
&species_parameters_0
&species_parameters_0

Note that nspec = 2

[David Dickinson]

Make sure we set the index for indexed namelists when allocating them in config_collection write

Should fix issue #177

→ <<cset b8dc0a703bca>>