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: 
There is not a way to do this without modifying the core. 

You should see `.php` files that are in subdirectories, but you won't see anything above the root theme directory for `.css` files, and you won't see any JavaScript files.

If you take a look at [`wp-admin/theme-editor.php`](https://github.com/WordPress/WordPress/blob/master/wp-admin/theme-editor.php), the relevant lines are...

```
<?php
$allowed_files = $theme->get_files( 'php', 1 );
$has_templates = ! empty( $allowed_files );
$style_files = $theme->get_files( 'css' );
$allowed_files['style.css'] = $style_files['style.css'];
$allowed_files += $style_files;

```

`$theme` is is a [`WP_Theme`](http://codex.wordpress.org/Class_Reference/WP_Theme) object representing the current theme. It's create a few lines above.

The `get_files` method searches a directory by matching the the file extension (first argument) and using the depth (second argument). The first call to `get_files` fetches all PHP files in the theme directory as well as the any subdirectories one level above the theme directory.

The second fetches all css files in the theme directory but it doesn't recursively go into subdirectories (notice the lack of the `$depth` argument).

There's not much you can do about this; there is a conspicuous lack of any calls to `apply_filters` and `do_action` in `theme-editor.php` and the `get_files` method lacks them as well. You're pretty limited.

And when PHP doesn't work, time to try the ugly JavaScript hacks!

Unfortunately, that's no good either. I tried exploring adding files to the list via JavaScript and ajax, but clicking on a JS added file results in an error message due to function called `validate_file_to_edit` which checks the current file to edit against the list of `$allowed_files` (see the above code that fetches that).
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.