Should I commit the contributed modules downloaded? Composer strongly recommends against. However, while they provide argumentation against there are also known workarounds if a project decides to do it anyway. Should I commit the scaffolding files? The drupal-scaffold plugin can download the scaffold files (like index.php, update.php, etc) to the html directory of your project. If you have not customized those files you could choose to not check them into your version control system.
Background Information Given WxT makes use of the Lightning base framework providing extensive integration with the Panels ecosystem of tools: CTools [Page Manager][page_manager] Panels Panelizer The following DrupalCon video serves as a great immediate introduction to the relevant concepts: