Re: Upgrading ships, etc?
You bet!
To upgrade facilities, just press the 'Upgrade' button on the colony screen. It will show you the new Version of any colony facilities you have on your planet.
To upgrade a ship, you must first design an upgraded ship. Then, you can actually upgrade the ship. To design your upgraded ship, go into the design window. Click on the ship and press Upgrade. This will leave your ship the same but upgrade, for example, Ion Engine I's to Ion Engine II's and Shield Generator I's to Shield Generator II's, etc. Or, you can just click on copy and then add/subtract as you wish.
Once you have a design you like, pick a ship that is at a spaceyard and click the Retrofit/Mothball button. It is green and looks to me like a recycle symbol. Click on the ship and press retrofit. It will then show you ship which are the same ship type--i.e. Light Cruisers.
It is possible you will get a message saying that the new design cannot differ by more than 50%. This means you are REALLY trying to upgrade the ship but the cost difference is greater than half. In this case, you can either leave the ship as it is, scrap it, or you can create an intermediate design between the old one and your desired one and retrofit it to that design first and then to your final design.
Hope that helps.
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