The Rambam says in Hilchos Shabbas 9,6Hilchos Shabbas 9,6 that smelting metal is bishula tolada of bishul, which does not answer your question.
It would seem that activities that could only be performed by the king or large organisations, such as quarrying, are not included in the 39 melachos which relate to the average individual's cessation from work.
Alternatively these activities may not be avos because the purpose of avos is to bring artefactsartifacts to a state where they are available for human consumption (in the broader sense of the word).
Because the end products of smelting, quarrying, etc. are far removed from human consumption we have not yet identified an av melacha.