Where to store JS and CSS that is not associated with a module? I've been given a ZIP file with the JS, CSS, HTML, and assets for a stand-alone jQuery application.  We would like to host this application through our Drupal 7 site hosted on Acquia Cloud.  I am looking for best practices on where to store this application. I've included additional info below but can supplement if there's other relevant info.  Can anyone suggest where I should store these files?

Due to some business-related decisions, we will always receive updates to this application in a ZIP file.  It may or may not receive updates. If it does, we'd like our content admin team to be able to manage it through Drupal or FTP.  It has not yet been decided if the application will be embedded in a page or accessed on it's own.

In our current site, we are not able to upload an entire directory and keep it in the same structure.  Each file must be uploaded manually.  We are fairly new to Drupal so I don't know if there is a module that would get us around this issue.

I am not allowed to make changes to the code or alter the directory structure (as that would require changes to the file references).

If there are no best practices for this, we can store it somewhere else and link out to it.  I would prefer to avoid this but if that's the recommended best practice, we can do it.
My gut feeling would be to place it in a folder in the root of your website and access it through a subdomain. I'm not sure, without knowing more about the application, if there is an effective way to integrate it with Drupal. It seems like it should stand on its own, in it's own directory structure, as it is a separate entity. I stand to be corrected here, but i don't see a problem with hosting it concurrently with your Drupal installation. It won't be manageable through the CMS, but without building the functionality in Drupal itself, it wouldn't be anyway.