Move workspace roots onto thread/session state and stop using active permission profile modifications as an overlay for writable roots. Existing app-server threads now preserve their persisted PermissionProfile value across resume, fork, and turn updates; permissions requests on existing threads only update the active named profile after validating it exists. Workspace roots can be updated independently, and SandboxPolicy::WorkspaceWrite no longer stores its own writable_roots.

codex-rs/thread-manager-sample/src/main.rs

@@ -202,6 +202,7 @@ fn new_config(model: Option<String>, arg0_paths: Arg0DispatchPaths) -> anyhow::R
         tui_keymap: TuiKeymap::default(),
         tui_vim_mode_default: false,
         cwd,
+        workspace_roots: Vec::new(),
         cli_auth_credentials_store_mode: AuthCredentialsStoreMode::File,
         mcp_servers: Constrained::allow_any(HashMap::new()),
         mcp_oauth_credentials_store_mode: OAuthCredentialsStoreMode::File,