Add --flake argument to nixos-rebuild

Use 'nixos-rebuild switch --flake .' to build from the flake.nix
in the cloned repository, resolving 'nixos-config not found' errors.

agent/src/agent.rs

@@ -304,6 +304,8 @@ impl Agent {
                 .arg("cm")
                 .arg("/run/current-system/sw/bin/nixos-rebuild")
                 .arg("switch")
+                .arg("--flake")
+                .arg(".")
                 .current_dir(working_dir)
                 .output()
                 .await