While experimenting with the reasoner command/operation. I noticed that the method just silently returns (and maybe event writes the result to a file) in case of an inconsistent ontology. There is no change in exit code (command-line level) or Java return value to indicate that there was an fatal problem.

In general we need an agreed up on mechanism to signal an error for a command (should we really use exceptions for this?). This should also result in a non-normal exit code for the command-line.