Question: I like to have folders in my theme folder for scripts and styles, but I can't access these folders in the "Edit Themes" interface. This is problematic for clients that don't give me FTP access. Is there a way to see these folders and the files in them from the Wordpress admin section?

Answer: 
The [Advanced Code Editor](http://wordpress.org/extend/plugins/advanced-code-editor) plugin provides this functionality. 

*From the plugin description:*

> 
> Enables syntax highlighting in the integrated themes and plugins source code editors. Supports PHP, HTML, CSS and JS.  
> 
>  Effectively edit your themes or plugins when you only have access to a browser, by enabling syntax highlighting in WordPress integrated source code editors. Supports PHP, HTML, CSS and JavaScript
> 
> 
> 

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**Edit:**
The plugin mentioned above doesn't seem to have the directory tree for themes; only plugins. There is, however, another plugin that *does* provide this functionallity: [WPide](http://wordpress.org/extend/plugins/wpide/)

*From the plugin description:*

> 
> File tree allowing you to access and edit any file in your wp-content folder (plugins, themes, uploads etc)
> 
> 
> 

There has also been a [trac ticket](http://core.trac.wordpress.org/ticket/4131) on this topic; hopefully this will be fixed in a future version of WordPress.
I do the same thing as you and organize things in folders. I never use that editor but I just took a look at one of my sites and I can see the files but not the directories. That is, the files are listed as present and are editable, but they are not displayed by directory. You can't tell what folder they are in unless you read the URL for the links.

If you are talking about a child theme, I am having trouble seeing some of the files and I don't know why. The owner, group, and permissions match on the parent theme, whose files I can see, and the child theme, some of whose files I can't see. I'd never noticed the issue until this question came up.