You have to set a regular expression (in the "Scan exclusion pattern" option) that will determine which files and folders will be ignored.
The expression is tested against the whole path of each scanned file and directory.
I usually use this tool to quickly test regexp when I need one.

Done.

Good. :)

Did you try to do a force refresh in your browser (usually shift + "refresh" button), or to clear your cache ?

Oops, I delivered the 1.8.1 a bit to quickly.
Here's 1.8.2.

Fixed. Version 1.8.1 is available.

You're right, I completely forgot to make the new reader compatible with the reverse proxy. I'll fix that soon.