refactor: Update Nix Flake, modules, and documentation
This commit refactors the repository, addressing the Nix Flake structure,
NixOS modules for Microcosm services, and documentation.
Key changes include:
- **Nix Flake and Packaging:**
- Modified `flake.nix` and `default.nix`.
- Removed `flake.lock` and `search` input.
- Added a `nurOverlay` for package integration.
- **NixOS Microcosm Modules:**
- Updated `constellation`, `pocket`, `reflector`, `slingshot`,
`spacedust`, `ufos`, and `who-am-i` modules with additional options,
systemd service configurations, user/group management,
tmpfiles, and security settings.
- Removed the `jetstream` module.
- Modified `quasar` to indicate its "Not Implemented" status.
- **Documentation:**
- Updated `AGENTS.md` with a structured project overview,
service usage details, and a Cachix cache section.
- Removed "Overlays" and "Reference Repositories" sections.
- **Project Structure:**
- Deleted `lib/default.nix` and `overlays/default.nix`.
- Removed `reference/` submodules (`blacksky.community`, `rsky`,
`tektite-cc-migration-service`).
- **Testing:**
- Added new test files (`tests/constellation-shell.nix`,
`tests/default.nix`) for the `constellation` service.
These changes modify the development and deployment of AT Protocol
services using Nix, adjust security configurations, and update documentation.