On the hlcsg line, add them like this:

hlcsg -wadinclude forest.wad -wadinclude trees.wad mapname
hlbsp mapname
hlvis mapname
hlrad mapname
....etc....

Or, to include ALL the wads without naming them, use -nowadtextures like this:

hlcsg -nowadtextures mapname
hlbsp mapname
hlvis mapname
hlrad mapname
....etc....