Move private runtime state outside checkouts and isolate worktrees

tests/test_bootstrap_entrypoint.py

@@ -48,13 +48,15 @@ def test_stdin_bootstrap_installs_verified_runtime_and_preserves_credentials(tmp
     server = ThreadingHTTPServer(("127.0.0.1", 0), Provider)
     thread = threading.Thread(target=server.serve_forever, daemon=True)
     thread.start()
+    workspace = tmp_path / "workspace"
+    workspace.mkdir()
     user_data = tmp_path / "user-data"
     user_data.mkdir(exist_ok=True)
     auth = user_data / "auth.json"
     auth.write_text('{"refresh_token":"synthetic-preserved"}')
     env = {"PATH": os.environ["PATH"], "NAPSEER_HOME": str(tmp_path / "runtime"),
         "NAPSEER_BIN_DIR": str(tmp_path / "bin"), "NAPSEER_USER_DATA_DIR": str(user_data),
-        "NAPSEER_PROJECT_ROOT": str(tmp_path), "NAPSEER_BASE_URL": f"http://127.0.0.1:{server.server_port}"}
+        "NAPSEER_PROJECT_ROOT": str(workspace), "NAPSEER_BASE_URL": f"http://127.0.0.1:{server.server_port}"}
     try:
         result = subprocess.run([sys.executable, "-"], input=(source / "nap_install.py").read_text(),
             cwd=tmp_path, env=env, capture_output=True, text=True, timeout=30)