At the very least, provide an example of the current way to exclude or include a single package from being instrumented.

Ideally, a user could select one or more modules to have clover enabled.
Similarly, the includes/excludes text boxes should be augmented with a File Chooser, or Package Tree Browser to make selecting a package as easy as possible.

Is it possible to put Clover in the Context Menu of the IDEA Package Explorer so that includes/excludes can be set from there as well?

Watching a new user trying to configure includes/excludes using the current UI is very revealing.