I commented this condition at lines 940-941:
if ( isset( $_wp_admin_css_colors[$current_color_scheme] ) )
$color = implode( ',', $rl->hex2rgb( $_wp_admin_css_colors[$current_color_scheme]->colors[3] ) );
And got the Media Library and the folders back. However that may not be the ideal solution.
Please help. 🙂