Just as an FYI, when creating a SharePoint exclusion rules for a file share, if you want to exclude documents in certain folders under the shared folder, you'll need to create two rules, i.e.: \\wfe1\docs\<foldername> and \\wfe1\docs\<foldername>\*.
I just got done testing this and it seems to work OK. I was unsuccessful at creating an inclusion rule that would allow me to exclude a folder as above, but then include a subfolder. The way exclusion rules are read, I'm not sure this would be possible.