update: bump 6 MCP packages + nixpkgs flake

- flake.lock: nixpkgs 2026-05-31 → 2026-06-16
- zotero-mcp: v0.2.2 → v0.5.0
- duckduckgo-mcp-server: 0.1.1-unstable → v0.4.0
- kindly-web-search-mcp-server: bump to latest commit + add trafilatura dep
- sabnzbd-mcp: pin to specific commit instead of refs/heads/main
- jellyfin-mcp: v2026.318.7 → v2026.604.2 (remove go.mod patch)
- nextcloud-mcp-server: v0.89.0 → v0.121.3

n8n-mcp, mcp-arr-server, pdf-reader-mcp held back:
upstream npm packages require @modelcontextprotocol/sdk versions
not yet published to npm registry

packages/duckduckgo-mcp-server/package.nix

@@ -6,14 +6,14 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "duckduckgo-mcp-server";
-  version = "0.1.1-unstable";
+  version = "0.4.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "nickclyde";
     repo = "duckduckgo-mcp-server";
-    rev = "d198a2f0e8bd7c862d87d8517e1518aa295f8348";
-    hash = "sha256-aoWU5AVErAt73V+BgveEmVnjNh/cteS+A9AIFLylOsw=";
+    rev = "v${version}";
+    hash = "sha256-g1mpBrhuCt3g/XnUfHoY8lJDMizINypikj8Lqk2LVuE=";
   };
 
   build-system = [ python3Packages.hatchling ];