Refine top-level exception handling.

If exceptions escape - they cause the whole stack trace to be printed (e.g. https://github.com/galaxyproject/planemo/issues/217#issuecomment-104306716) - I would expect this behavior if `-v` has been supplied - but for normal execution probably this should just catch the exception and `planemo.io.error(str(e))` and then exit with a non-zero exit code.