refactor: remove dead code, extract shared agent options, optimize flake

- Remove dead overlays/default.nix (flake defines overlays inline)
- Remove orphaned overlays/mods/{beads,n8n}.nix (never imported)
- Remove docs/packages/notesmd-cli.md (package doesn't exist)
- Extract externalSkills submodule to shared-options.nix (eliminates
  ~100 lines of duplication across opencode/claude-code/pi modules)
- Fix lib output: use nixpkgs.lib directly instead of instantiating
  a full nixpkgs just to get lib
- Add lib unit tests to flake checks
- Update stale comment in coding-rules.nix

lib/coding-rules.nix

@@ -1,4 +1,4 @@
-# Opencode rules management utilities
+# Coding rules management utilities
 #
 # This module provides functions to configure Opencode agent rules across
 # multiple projects. Rules are defined in the AGENTS repository and can be