Everything free starts in the same place: clone the yard, grow a hull, muster a crew.
Clone the yard: one incantation grows the hull and musters a crew — a Captain in the ready room, a First Officer on the bridge, a Ship's Engineer in the engine room and a Doctor on watch. Every room answers on its own hailing frequencies, all of them on subspace, and the channel is opened to the whole complement for you.
The Captain's own kit, serving planetside: installed directly, no hull anywhere in sight. Readymax is a package-rich, native-compiled species that stands perfectly well on its own — it is the ready room of a Basilisk ship, and it is also just a good Emacs.
You cannot lay down a hull from the Captain's cabin; that is deliberate, and it is the yard's business.
Cyclops ($99) fits a transporter room, pre-staffed with its Chief; Eyes Only ($69) fits the radio shack, with its Communications Officer. Both are sold by Gornskew Enterprises and slot into an existing hull. A ship comes up without either, and routing by hand with docker ports stays open if you would rather.
Gornskew lays down the ship and grows the engine species she carries — the open-source Gendl line, ready-grown and published for any yard to draw on. For commercial engines and their licensing, see genworks.com.