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1. Can you repair ships while in combat?
You can not repair ships in combat. I think the regen tech for organics may repair but I have never played that race.
Yes, Organic Armor will repair itself if it hasn't been totally destroyed. Some mods add this ability to other components.
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3. Can I choose to upgrade the facilities on just a couple of planets instead of on all of them?
Yes, with a little work. You can hit the Upgrade Facilities button, then go to each planet's build queue and delete or rearrange the Upgrade entries, or put the planet's queue On Hold. When upgrades are available, there will be a button for them on the planet's Construction Queue, as well.
If for some reason you only want to upgrade some of the same kind of facility on one planet, you have to scrap the old facility and build the new one.
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4. When I use intelligence, what's the difference between the different levels? And is there any reason why I shouldn't have an intelligence program running all the time?
The higher levels can accumulate more points, so they take longer to "complete". Completing an intel project erases all the points you've committed to it, so you want to avoid that if possible. Also, there's at least one high level attack that Counterintel 1 can't store enough points to block.
You might occasionally want to put all your intel production into attacks, but in general, keeping Counterintel going is a good idea.
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6. Can you find things on planets when you colonize them? Some of the planets have descriptions like "The final resting place of two ancient races", which makes me think that you might.
A planet with the Ruins icon can give you levels of technology, or a unique tech that can't be researched otherwise. These planets will show on the (F4) Planets/Special list.
[ 20 April 2002: Message edited by: capnq ]