Fix for issue #910

This fix includes new Permission Denied error handling for trying to run commands that are not executable.

I plan on keeping #910 open for other vague error messages that occur in the program (like ion: expansion error: Could not expand subprocess: pipeline execution error: command not found: im_not_a_command from pipelines.ion in the tests) as I think this is not that great of an error message. It gives no line number or anything of the sort. It is more useful for debugging ion itself than debugging your scripts.