Ok, the way ships are purchased and stored has been changed slightly. So please make note of the change before you do anything with the shipyard.
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Buying a new Ship
When you buy a new ship it is stripped bare. NOTHING from your previous ship is transfered to your new ship.
If you are not storing your previous ship or it is a pioneer then everything on that ship is SOLD at market prices and you get the money for those items. This includes the following items: ore, goods, organics, energy, colonists, fighters, torpedoes, armor points, warp editors, genesis devices, emergency warps, escape pods, fuel scoops, novas and mine deflectors. You will receive market value for those items.
If you are storing your previous ship then ALL of those items will stay on that ship and will NOT be moved to your new ship.
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Swapping ships from Storage
If you are swapping your current ship with one you have in storage then NOTHING transfers between ships.
If your current ship is a pioneer then everything on that ship is SOLD at market prices and you get the money for those items. This includes the following items: ore, goods, organics, energy, colonists, fighters, torpedoes, armor points, warp editors, genesis devices, emergency warps, escape pods, fuel scoops, novas and mine deflectors. You will receive market value for those items.
These changes should make more sense to people. Also, when selling your ship back or losing a pioneer usually resulted in the items mentioned above being lost. You now receive money back for them. Also Market Values are usually HALF the price you paid for the item.
