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

AGENTS.md

@@ -251,6 +251,33 @@ When modifying overlay behavior:
 - [Nix Flake Patterns](https://github.com/NixOS/flake-patterns)
 - [Rust in Nixpkgs](https://nixos.org/manual/nixpkgs/stable/#rust)
 
+## Updating Packages
+
+Use [nix-update](https://github.com/Mic92/nix-update) to bump versions and update hashes:
+
+```bash
+# Update a package to the latest version
+nix-update <package-name>
+
+# Update to a specific version
+nix-update <package-name> --version <version>
+
+# Update a package pinned to a commit hash (e.g. skillsmcp)
+nix-update <package-name> --version=branch=main
+```
+
+After updating, always test the build:
+
+```bash
+nix build .#<package-name>
+```
+
+### Package-Specific Notes
+
+- **goose-cli**: Also updates `librusty_v8` hashes automatically via the custom fetcher
+- **mcp-gateway**: Standard Rust package, `nix-update` handles version + cargoHash
+- **skillsmcp**: Pinned to a commit hash; use `--version=branch=main` or specify the target commit with `--commit`
+
 ## Git Workflow
 
 ### Committing Completed Work