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

flake.nix

@@ -77,10 +77,7 @@
     };
 
     # Library functions - helper utilities for your configuration
-    lib = forAllSystems (system: let
-      pkgs = pkgsFor system;
-    in
-      import ./lib {lib = pkgs.lib;});
+    lib = forAllSystems (system: import ./lib {lib = nixpkgs.lib;});
 
     # Development shells for various programming environments
     # Usage: nix develop .#<shell-name>
@@ -104,6 +101,9 @@
           ${pkgs.alejandra}/bin/alejandra --check ${./.}
           touch $out
         '';
+        # Lib unit tests
+        lib-agents = import ./tests/lib/agents-test.nix;
+        lib-coding-rules = import ./tests/lib/coding-rules-test.nix;
       });
 
     # Templates for creating new packages/modules