Scripts are more or less pieces of text (though you access it through a special editor) that tells the game "these things should happen" when they are run. They are run by calling them from another script, or the last page of a trigger can specify "run script" with the name.
(Similar to "doctrine script" is "doctrine conditions" which can set extra conditions for a trigger, and "platform doctrine" which are stored in the doctine\ directory, governing platforms behaviour across missions.)
The refresh loadout script command, as I've heard it, will, for air platforms only, give you access to the loadout screen mid-flight, so you can refill torpedoes, buoys and such. I'm not totally sure about this though.
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