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In ship command menu there are a couple lines for additional commands, but they all show "inactive" and when I click on it all all it shows is inactive. What is it for? Do I need a given software to unlock that? A ship category?...

Also for player stations, there's about 10 lines for commands (in advanced menu) but all show inactive too. Here I get 3 options: inactive, signal incoming ships (which only seem to work instantly? so not a way to be alerted from attacks or something, maybe to check if ships have decided to come here and trade?), and transfer credits.

So why are there so many lines if there are not more options? Is there a way to get more commands somehow?

I think the only one that stays active is a command to automatically transfer credits when the station's wallet reaches a threshold.

There aren't a lot of them, but mods use them at times.

Yes and yes.

Both ships and stations have "additional command" slots, (2 and 10, respectively). Shiptype and equipment does affect available commnads. Bonuspack scripts add some for stations too.

The commands are either "one-shot" or "background services". A one-shot starts, does quickly one specific thing, and quits. A service keeps running on the slot until it is stopped (or replaced).

Examples:

Stations:
Report incoming ships is a one-shot.
Automatic money transfer is a service.
(CAG) Trade Barrier is a service.

Ships:
Missile Defence Mosquito is a service.
Lauch all marines is a one-shot.
Missile Barrage is a one-shot.

Note that you can run additional commands on a ship without disrupting the main (autopilot) command that the ship is running.