I would like the AI to keep the buildings it captures (particularly superweapons) but the AI always seems to sell them every time they capture them. Is this hard coded into the game or can I change this from editing the scripts?

yep.

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Oh ok what a shame because it would be nice to change that. Is it also possible to make the AI 'force attack' something like the ground or maybe its own units?

You can only tell AI to attack objects, so if you want them to attack at a waypoint spawn a named invisible object at that location and make it fire agaisnt that.

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Actually, it is possible to make the AI force fire. I just found out a few days ago.

You have to add this command button:

[???] Command button: 'Command_BattleshipFire' is added to all objects of type 'AmericaVehicleChinook' in slot number 11 (1-12).

After adding the command button (to any object, really) you can "use command button on object" this command button to force fire stuff.