Can buff entities be applied to certain ships without using invaluable ability slots? For example, a hidden buff that disables the jump drives of all frigates or just specific types of frigates. I mean "hidden" as always applied to the ships without using one of the four ability slots, and still showing up on the infocard "Phase Jump Disabled." Or a buff that increases mitigation.
I've done quite a few of these, but you need ways to get them on the ships. See AbilityJemHadar in SOA2 for an example. It restricts the Jem'Hadar related abilities to only their ships, excluding the Cardassians and Breen.
Can planets be made to generate a set amount of crystal, metal, and credits? What about buildings and Starbases?
Yes, but this could be a very bad idea. There are buffs you can use to create resources and money, but you need to be careful about throwing periodics on everything for CPU utilization reasons.
Can ships (such as the Constructor Frigate) be made to start constructing items in a gravity well, even if it's not colonized?
No. Construction via the constructor frigates is a hardwired behavior, you can only "build" through the menu that requires an owned planet to access. You can however build without them using abilities to spawn specific structures with a ship.
Is it possible to construct buildings through a Starbase?
Yes, indirectly. You could construct buildings with an ability. You'd spawn a frigate with an ability, and then use that frigate to make the structure desired.
Where is the location of the Neutral Extractor in the files?
I believe that is the TECH version of the extractor.