refactor(agents): scope customization to monorepo

Move Pi runtime resources into project-local .pi directories and keep shell modules responsible for installing Pi, Herdr, gitea-axi, and Pi package patches.

Remove legacy global agent context, Claude Code customization, the global skills bridge, and the external skills flake input.

configs/nixos/modules/shell/herdr.nix

@@ -18,6 +18,8 @@ in
     home-manager.users.${user} = {
       home.packages = [ pkgs.herdr ];
 
+      # Refresh the vendored project-local Pi extension from the monorepo root.
+      # Run `PI_CODING_AGENT_DIR=$PWD/.pi herdr integration install pi`.
       xdg.configFile."herdr/config.toml".text = ''
         [keys]
         prefix = "ctrl+space"