Within this area:
Design > Responsive & Mobile Design
I opened the "Smart Phones & Small Devices" rule group and chose "Transform the layout" and selected a CSS file to transform the layout under "Specific CSS file for transforming layout and design".
Upon saving that, I realized the location that the system puts in includes ~/App_Data/ as part of the location of the file. And it appears that it also adds /App_Data/ to the CSS <link> tag, but the file doesn't load with /App_Data/ as part of it's URL...
So I figured, I'd just add the CSS as a standard part of my Master Page and ditch the CSS file link in the Responsive & Mobile Design settings.
...but... There doesn't seem to be any way to remove a CSS file linked there after it has been added...
How can I get rid of that?
I just want to note that with the new release you will have the ability to choose the pages and templates on which the responsive design rule will be applied.
You can do two things:
Remove the rule entirely and recreate it from scratch without linking to a .css
Open SQL Management Studio, find the [sf_rdsgn_media_query] table and then set the value for the [additional_css_file_path] to NULL (ctrl+0).