I use wordpress API outside of the wordpress installation (example.com/blog/). Namely, I use it on the index page of my site (e.g. http://example.com/ or http://example.com/index.php).
In the WP-SuperCache settings I have "index.php" in the Rejected URIs, but it still caches it.
Is it possible to reject URIs outside of the /blog/ directory where wordpress is installed? Or perhaps can you add an option to not cache files outside of the wordpress directory?