I, too, am getting "Component Install: Another Component is already using directory: '[path]/components/com_joomdoc' and "Component Install: Another Component is already using directory: "[path]/administrator/components/com_joomdoc'" messages trying to upgrade from 2.0.2 to 3.
Actually, I'm not 100% convinced I'm even at 2.0.2 -- I started with 2.0.1 and later unzipped the 2.0.1-to-2.0.2 patch... but Extension Manager still reports that I'm at 2.0.1.
I am hesitant to try uninstalling 2 prior to installing 3, because I don't know if by doing so I will lose my 100+ joomdocs.