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

overlays/mods/beads.nix

@@ -1,16 +0,0 @@
-{prev}:
-prev.beads.overrideAttrs (oldAttrs: rec {
-  version = "0.47.1";
-
-  src = prev.fetchFromGitHub {
-    owner = "steveyegge";
-    repo = "beads";
-    tag = "v${version}";
-    hash = "sha256-DwIR/r1TJnpVd/CT1E2OTkAjU7k9/KHbcVwg5zziFVg=";
-  };
-
-  vendorHash = "sha256-pY5m5ODRgqghyELRwwxOr+xlW41gtJWLXaW53GlLaFw=";
-
-  # Tests require git worktree operations that fail in Nix sandbox
-  doCheck = false;
-})

overlays/mods/n8n.nix

@@ -1,18 +0,0 @@
-{prev}:
-prev.n8n.overrideAttrs (oldAttrs: rec {
-  version = "2.4.1";
-
-  src = prev.fetchFromGitHub {
-    owner = "n8n-io";
-    repo = "n8n";
-    rev = "n8n@${version}";
-    hash = "sha256-EQP9ZI8kt30SUYE1+/UUpxQXpavzKqDu8qE24zsNifg=";
-  };
-
-  pnpmDeps = prev.pnpm_10.fetchDeps {
-    pname = oldAttrs.pname;
-    inherit version src;
-    fetcherVersion = 1;
-    hash = "sha256-Q30IuFEQD3896Hg0HCLd38YE2i8fJn74JY0o95LKJis=";
-  };
-})