... a theory is a group of hypotheses that make claims about what kind of entities there are and how those entities change over time and interact with each other. If you like, the theory contains claims about ontology and laws. If you prefer, the theory tells you what kind of stuff there is and how that stuff behaves.
That's a really odd way to think of theories. I reckon a theory is something that is both sufficiently broad and sufficiently tested that a scientist can use it to figure out how to frame a question in a testable manner.
For example, if you're looking into an outbreak of a drug resistant germ, you can use the theory of evolution to design an experiment that will test how this resistance arose, and how effective it is against other drugs.
Now, I don't think these two descriptions of a theory are necessarily contradictory, although the theory-as-set-of-hypotheses I'm describing might not be well tested (i.e., it could be a new theory). Indeed, it seems like having some picture of what kind of stuff you're dealing with and some of the ways that stuff behaves it at least extremely helpful, if not absolutely necessary, to the framing of questions in a testable manner.
The thing that interests me here is the possibility that scientists think of "theory" in a different way than the philosophers of science who are trying to make sense of what scientists are doing. So, a question to the scientists: How would you define (or at least describe) a theory? If you think it's relevant (and it may well be), indicate your scientific field.
Once we have some "empirical data" on this, I'll give you my hunches as to what may be behind some of the differences in perspective.