I have the following structure for my web app

Code:

/src/java  -> java source files /src/conf -> resources like properties files /src/groovy -> groovy source files /src/web -> my webroot

I'd like the contents of src/conf and src/groovy to be deployed to the WEB-INF/classes directory whenever I make changes to them. I tried adding them as "Class folders" in the "Java Build Path"/Libraries but this did not seem to work.

Is there a way to do this?

Remove them from your libraries list, and instead go to the Source tab and add them as Source folders, Eclipse will automagically copy the contents to the output folder on build.