Sets such as Automaton shares the common "damage to your (Physical) abilities" tooltip language and it buffs your Stamina Light Attacks. Similarly, Netch will buff your Lightning Staff Light Attacks. And so on.
"Abilities" is usually a loose term that means basically any action that the player takes, which is broad but it also means that it does not apply to proc sets and such.
But as a rule: if it is YOU who are doing/casting it, then it is an ability.