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/pi/default.nix

@@ -0,0 +1,48 @@
+{
+  config,
+  lib,
+  pkgs,
+  ...
+}:
+# Pi, a terminal coding agent, for the primary user, configured through
+# home-manager, which ships the package and manages global settings.
+# The login credential is left unmanaged, so it survives rebuilds.
+let
+  cfg = config.modules.shell.pi;
+  user = config.user.name;
+  piDir = "${config.users.users.${user}.home}/.pi/agent";
+  patchedPi = pkgs.pi-coding-agent.overrideAttrs (old: {
+    patches = (old.patches or [ ]) ++ [
+      ./patches/pi-flex-spacer.patch
+      ./patches/pi-tool-lookup-validation.patch
+    ];
+  });
+in
+{
+  options.modules.shell.pi = {
+    enable = lib.mkEnableOption ''
+      Pi, a terminal coding agent, configured through home-manager'';
+  };
+
+  config = lib.mkIf cfg.enable {
+    home-manager.users.${user} = {
+      programs.pi-coding-agent = {
+        enable = true;
+        package = patchedPi;
+
+        settings = {
+          defaultProvider = "openai-codex";
+          defaultModel = "gpt-5.5";
+          defaultThinkingLevel = "medium";
+          theme = "dark";
+          enableInstallTelemetry = false;
+          enableAnalytics = false;
+        };
+      };
+
+      # The first declarative rollout replaces the interactive settings file.
+      # Login state stays in auth.json, which this module does not manage.
+      home.file."${piDir}/settings.json".force = true;
+    };
+  };
+}