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Despite what everyone thought, it had not started as something intentionally related to the codename he’d been given. Rather, it was a function of how he was often stationed in high places for long periods of time - you had to keep hydrated, and well nourished, and have proper clothing for changes in weather. After a certain period, when he had been assigned several long stakeouts in a row, he realized there was no point in climbing down to sleep - especially when he was likely to be roused and expected to be in position if his mark was moving. So he started bringing a sleeping bag with him, and then books and a gameboy and a mini DVD player for when he wasn’t on watch. He knew, before the first agent decided he was going to be clever, that people would consider it a nest.
Self-awareness was more than half the battle. That, and the ability to shoot unsuspecting agents in the ass with an arrow when they began to annoy him.
Clint moves into Avengers Tower, and promptly takes up residence in the air ducts, including the one above Bruce's lab. It soon becomes clear that this isn't just a cracky, quirky behavior.
- Part 1 of Adaptations