fix anti-patterns: niri portals, nix optimise, zram; add dev packages

- niri: remove explicit package override (use niri-flake default), drop
  KDE portal, set xdg.portal.config for deterministic portal resolution,
  remove unused waybar
- core: replace synchronous auto-optimise-store with async
  nix.optimise.automatic, reduce zramSwap.memoryPercent from 300 to 100
- dev: add python3 and uv to system packages
- add .mcp.json (nixos MCP server) and CLAUDE.md

modules/dev.nix

@@ -12,6 +12,8 @@ in {
     environment.systemPackages = with pkgs-unstable; [
       # CLI utilities
       gcc
+      python3
+      uv
       fzf
       just
       tree-sitter