Generate `.agents` at the setup script

The content of `.agents` folder is duplicated from what provided in root, and there is minimal costs of generating them at the `setup` script in consumer machines and `.agents` is not yet a standard like `AGENTS.md`

**Background**:

I'm currently trying to integrate `gstack` into [crabtalk][crabtalk]'s package manager, the duplicated skills detection bothers me a lot, I can optimize the setting up script for gstack in our fork but I believe we can slim this in gstack as well since it is confusing even just looking at the source code

[crabtalk]: https://github.com/crabtalk/crabtalk