Categorising themes by folders in backend

I want to organize themes like:

1. wp-content/themes/themeshop/theme1
2. wp-content/themes/themeshop/theme2
3. wp-content/themes/themeshop/theme3

Now from my understanding, this organization works perfectly at the folder level. I dropped themes in subdirectories and everything seems to work fine. Now is it possible to duplicate this categorization in the Administration backend on the themes page?

_{Updated plugin version available at GitHub.}

I first saw your Question at [wp-hackers] list, and, after implementing the solution, was about to publish a Q&A for that. Well, it’s already here, and has a bounty put on it 🙂

As Daniel Bachhuber points out in the thread:

WordPress.com puts themes inside of subdirectories

/wp-content/themes/public 
/wp-content/themes/premium

I came up with this solution to show that in the backend:

• in Multisite, we can add a column in the Themes’ screen and show the info with manage_themes_custom_column and manage_themes-network_columns.

• in single sites installations, the only entry point I found was in theme_action_links.

<?php   
/**
 * Plugin Name: Theme Folders Categories
 * Plugin URI: http://wordpress.stackexchange.com/q/96361/12615
 * Version: 1.0
 * Author: Rodolfo Buaiz
 * Author URI: http://wordpress.stackexchange.com/users/12615/brasofilo
 * License: GPLv2 or later
 */
class WPhackersSE_Theme_Folders
{   
    public function __construct()
    {
        add_action( 'plugins_loaded', array( $this, 'start_up' ) );
    }    

    /**
     * Hooks for Network themes and Single Site themes
     * Nothing happens on sub-sites of a Network 
     */
    public function start_up()
    {
        if( is_network_admin() )
        {
            add_filter( 'manage_themes-network_columns', array( $this, 'column_register' ) );
            add_action( 'manage_themes_custom_column', array( $this, 'column_display' ), 10, 3 );
            add_action( 'admin_head-themes.php', array( $this, 'network_theme_category_css' ) );
        } 
        elseif( !is_multisite() )
        {
            add_filter( 'theme_action_links', array( $this, 'theme_folder_single_site' ), 10, 2 );
            add_action( 'admin_head-themes.php', array( $this, 'theme_category_css' ) );
        } 
    }

    /**
     * Add custom category (folder) column in network themes
     * 
     * @param array $columns
     * @return array
     */
    public function column_register( $columns ) 
    {
        $columns['theme_folder'] = 'Category';
        return $columns;
    }

    /**
     * Display custom row in network themes
     * $stylesheet contains a string "folder/theme_name"
     * $theme is a WP_Theme object
     * 
     * @param string $column_name
     * @param string $stylesheet 
     * @param object $theme 
     * @return string
     */
    public function column_display( $column_name, $stylesheet, $theme ) 
    {
        if( 'theme_folder' != $column_name  )
            return;

        echo $this->make_button( $stylesheet );
    }

    /**
     * Adjust column width and button style in Multisite screen
     */
    public function network_theme_category_css()
    {   
        echo "<style type="text/css">
            #theme_folder { width: 10% }
            {$this->button_style()}
            </style>";
    }

    /**
     * Show theme category (folder) in single site theme action row
     * $theme is a WP_Theme object
     * 
     * @param array $actions
     * @param object $theme
     * @return array
     */
    public function theme_folder_single_site( $actions, $theme )
    {
        array_unshift( $actions, $this->make_button( $theme->stylesheet ) );
        return $actions;
    }

    /**
     * Adjust button style in Single site screen
     */
    public function theme_category_css()
    {   
        echo "<style type="text/css">{$this->button_style()}</style>";
    }

    /**
     * Common button for Multi and Single sites
     * The category name is extracted from a string "folder/themefolder"
     * 
     * @param object $theme
     * @return string
     */
    private function make_button( $stylesheet )
    {
        $button_category = sprintf( 
            '<a href="javascript:void(0)" class="button-secondary theme-folder" title="%1$s">%1$s</a>',
            dirname( $stylesheet )
        );
        return $button_category;
    }
    
    /**
     * Common style for Multi and Single sites
     * 
     * @return string
     */
    private function button_style()
    {
        return '.theme-folder { 
            cursor: default !important;
            line-height: 15px !important;
            height: 17px !important;
            background-image: -webkit-gradient(linear, left top, left bottom, from(#DCFEDE), to(#CBEBCD)) !important;
            background-image: -webkit-linear-gradient(top, #DCFEDE, #CBEBCD) !important;
            background-image: -moz-linear-gradient(top, #DCFEDE, #CBEBCD) !important;
            background-image: -o-linear-gradient(top, #DCFEDE, #CBEBCD) !important;
            background-image: linear-gradient(to bottom, #DCFEDE, #CBEBCD) !important;
        }';
    }
}

new WPhackersSE_Theme_Folders;

Result in Multisite:
Folders /themes/clientes/ and /themes/brasofilo/). There’s no output in sub-sites of the network.

Much probably it’s possible to add a filter here.

Result in a single site:
Multisite not enabled. Folders /themes/defaults/ and /themes/others/.

This screen is really limited in terms of customization. I agree with @Ralf912 analysis.

Important note: after moving active themes into sub-folders, all sites lose its theme configuration, each site theme has to be set again.