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I have been searching for a long while now and can get no concrete opinion. At the start of the civil war which forts contain Imperials if the player is allied with the Legion?

This is before activating dragons (which I am loathed to do). It seems they all have bandits etc in them, and even after clearing them they just respawn with more bandits.

Thanks for any answers

Pretty sure all of those war maps you find with the flags on them mark all of the army-occupied forts.

Based on the listing of forts as targets for Stormcloak missions from the 'Liberation of Skyrim' quest page I'd say probably:

Neugrad, Sungard, Snowhawk and (assuming you've done the first Legion quest) Hraggstad.

Imperials tend to turn up in Greymoor Fort in Whiterun Hold as well (although that might only be after the Battle for Whiterun).

tbh best way to tell for sure would be to start a new game on easy and just bomb around quickly and check for yourself.