fix: improve package quality and fix goose-cli build

- Add meta.platforms to all packages for proper platform detection
- Add passthru.category to mcp-gateway for consistency
- Fix meta style inconsistency in mcp-gateway (lib.licenses → licenses)
- Fix pythonImportsCheck in skillsmcp to actually validate the import
- Remove empty maintainers list from skillsmcp
- Add libclang to goose-cli nativeBuildInputs (fixes bindgen/llama-cpp-sys-2 build)
- Add treefmt.toml with nixfmt formatter configuration
- Add nixConfig.extra-substituters for binary cache support
- Delete broken goose-cli/update.py (referenced missing scripts/updater.py)
- Document nix-update usage in AGENTS.md for package updates
- Fix stale project structure diagram in README

README.md

@@ -95,13 +95,16 @@ nix develop
 ```
 nix-overlay/
 ├── flake.nix                    # Flake definition
+├── treefmt.toml                 # Code formatting configuration (nixfmt)
 ├── overlays/                    # Overlay implementations
 │   ├── default.nix             # Binary-cache-friendly overlay
 │   └── shared-nixpkgs.nix      # Dependency-sharing overlay
 ├── packages/                    # Package definitions
 │   ├── default/                # Meta-package listing all packages
-│   ├── goose-cli/              # Goose CLI package
-│   └── flake-inputs/           # Utility for caching flake inputs
+│   ├── flake-inputs/           # Utility for caching flake inputs
+│   ├── goose-cli/              # Goose AI agent CLI
+│   ├── mcp-gateway/            # MCP protocol gateway
+│   └── skillsmcp/              # MCP server for Agent Skills
 └── README.md
 ```