What determines when a location is 'CLEARED' on the map?
Solution 1:
Fallout 4 uses the Creation Engine, previously used in The Elder Scrolls V: Skyrim. (source)
In Skyrim, an area became cleared if you killed the boss in that area or most of the enemies in the area. (reference)
This behavior appears to have stayed the same for Fallout 4.
Solution 2:
In Skyrim, an area became cleared if you killed the boss in that area or most of the enemies in the area.
Don't see why it should be any different in Fallout 4.