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I start in X3: Albion prelude as a Humble Merchant. It starts with a ship called Mercury and another called the Discoverer.
I have travelled to the shipyard in Argon Prime, but I don't have any idea how to sell my ships.
How can I use the Discoverer? I haven't found a way to switch to the Discoverer cockpit. Am I allowed only to give it follow commands?
A) In stations
You dock both ships inside a station and then you can switch over to a ship by selecting it in the menu (docked ships) and pressing X.
B) In space
Fly close to your ship, press the button to eject your current ship and then travel carefully to your other ship. Press "e" (default) to enter the ship. Make sure your current ship comes to a FULL halt before leaving it! :D Otherwise it might bounce you away or even kill you, depending on it's size ;).
To add onto the other answer, there are also several other ways to remotely command ships.
To increase the type and number of remote commands, you have to buy certain software for them. For instance, navigation command software allows you to give them orders to go to a sector or dock at a remote station.
To remotely sell and buy things (including ships), the ship you are in must have the trading system extension software installed and you must have a presence in that sector (the ship you are trying to sell is considered a presence so you can do it remotely).
The only place you can sell ships is at the shipyard. To sell it in the early game, both you in the mercury and your discoverer must dock at the shipyard, then you can either switch ships or sell it.
