I think there should be an easy way to change all WordPress-specific links in the source code - update-persistent way to select own paths for:
> wp-admin (not only by changing and hiding through plugins - WordPress even doesn't have any Captcha or try-limit bruteforce-login protection built in, this also has to be added via plugins)
> wp-content (not only a moving ability for wp-content/uploads folder)
> wp-includes (as far as I know there is no user-friendly or even developer-friendly way to change this, just hardcoding, which is update-destructive).
The top would be a customization of wp-content/plugins & wp-content/themes folder paths.