Well this is a little tricky part of CMK 
Three Steps
- Collect the Files (Agent)
- Group the Files (Site)
- Add rule to the group (Site)
If you have Enterprise Edition, you can config the Agent with the Bakery to collect wanted files. After the Agent sends the Data from the Files to CMK Site, you can work with it. Group files by name, extension… what ever. And this groups gets names, on this names the rule you have in the beginning of the thread targets.
But i think, you will run in an other problem. An empty folder will not work for a “zero” count if needed. An empty folder just let the service for the file group disappear…
