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

modules/home-manager/coding/agents/shared-options.nix

@@ -0,0 +1,75 @@
+# Shared option definitions for agent modules.
+# Prevents copy-pasting the externalSkills submodule across opencode/claude-code/pi.
+{lib}: let
+  inherit (lib) mkOption mkEnableOption types literalExpression;
+in {
+  # Common agentsInput option used by all agent modules.
+  mkAgentsInputOption = description: mkOption {
+    type = types.nullOr types.anything;
+    default = null;
+    inherit description;
+  };
+
+  # Common modelOverrides option.
+  mkModelOverridesOption = mkOption {
+    type = types.attrsOf types.str;
+    default = {};
+    description = ''
+      Per-agent model overrides. Maps agent slug to model string.
+      Example: { chiron = "anthropic/claude-sonnet-4"; }
+    '';
+    example = literalExpression ''
+      {
+        chiron = "anthropic/claude-sonnet-4";
+        "chiron-forge" = "anthropic/claude-sonnet-4";
+      }
+    '';
+  };
+
+  # External skills submodule — used by opencode, claude-code, and pi modules.
+  externalSkillsOption = mkOption {
+    type = types.listOf (types.submodule {
+      options = {
+        src = mkOption {
+          type = types.anything;
+          description = "Flake input pointing to a skills repository root.";
+        };
+        skillsDir = mkOption {
+          type = types.str;
+          default = "skills";
+          description = ''
+            Subdirectory inside src that contains skill folders.
+          '';
+        };
+        selectSkills = mkOption {
+          type = types.nullOr (types.listOf types.str);
+          default = null;
+          description = ''
+            List of skill names to cherry-pick from this source.
+            null means include every skill found in skillsDir.
+          '';
+        };
+      };
+    });
+    default = [];
+    description = ''
+      External skill sources passed to mkOpencodeSkills.
+      Each entry maps directly to an element of the externalSkills
+      list accepted by the AGENTS flake's lib.mkOpencodeSkills.
+    '';
+    example = literalExpression ''
+      [
+        { src = inputs.skills-anthropic; selectSkills = [ "claude-api" ]; }
+        { src = inputs.basecamp; }
+      ]
+  '';
+  };
+
+  # Helper to map externalSkills from module config to mkOpencodeSkills format.
+  mapExternalSkills = cfgEntries:
+    map (
+      entry:
+        {inherit (entry) src skillsDir;}
+        // lib.optionalAttrs (entry.selectSkills != null) {inherit (entry) selectSkills;}
+    ) cfgEntries;
+}