rdfcat and owl:imports/owl:Ontology

My ontological structure is developed in modules wired together with owl:imports triples. My production environment requires a single file. I have tried using rdfcat to flatten the system - without success so far. Multiple owl:Ontology triples are in the final file as one unresolved owl:imports triple. To get rid of the import triple, I have tried running the mostly-flattened file back through rdfcat but that didn’t do the trick. I have tried rdfparse thinking I could run it through sed - again without success ( error: (line 1 column 1): Content is not allowed in prolog.). Any suggestions for producing a single file with only the top-level owl:Ontology intact and all owl:imports statements resolved (guess that’s a little redundant)? Protege’s merge functionality does it but I need to do it from the command line.

Thanks.