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/zotero-mcp/package.nix

@@ -39,14 +39,14 @@ let
 in
 python3Packages.buildPythonApplication rec {
   pname = "zotero-mcp";
-  version = "0.2.2";
+  version = "0.5.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "54yyyu";
     repo = "zotero-mcp";
     rev = "v${version}";
-    hash = "sha256-GZkzABsUh6qua66K4URPq0InLgs6cqLgKEXm7wzT+s8=";
+    hash = "sha256-ioy6bdP+jFioUGBKiiYtD4nbdFe6v2E3nCi6s9+dTT0=";
   };
 
   build-system = with python3Packages; [