The theme editor is located under /wp-admin/theme-editor.php and uses get_current_theme(); to give you the first files to edit. From the returned array of theme data, it uses 'Template Dir' to locate the directory and 'Template Files' to give you a list of files to edit (loops through the files with a foreach loop). For stylesheets it uses 'Stylesheet Dir' and 'Stylesheet Files' to loop through.
Point is that:
1. there are no filters or hooks, so you’d need to modify core directly (which is not recommended, as your changes would be overwritten on update) and
2. you’d need to write a function that reads the whole folder, finds all subfolders and then another one to find all containing files and last loop through them too.
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