Once --source is specified, --include is ignored. If the user specifies both, this shouldn't happen silently. A warning or error is appropriate.
Would an appropriate fix be to issue a warning (but then still return True) in CoverageScript.args_ok?
@alonghi Unfortunately, the conflict could be in the configuration file also. And run uses with --source or --include, but "report" uses only --include. I'll have to think more about what is a problem here, and what to do about it.
addressed this issue on the github mirror with a proposed PR #9