Improved update_attributes and flag setting

Curious to see if you'd approve of this work before I go ahead with `getpax`/`setpax`. This sets the foundation down with a few improvements to `update_attributes`.

- renamed apply to set_pax_flags and introduced get_pax_flags
- moved flag validation into set_pax_flags so it can be reused
- reorganized and condensed logic in update_attributes
- dropped line_ignored for warnx
- update_attributes now returns an exit status