Create a pruning run() method that ignores end-points inside a ROI
This should make it easier to achieve tferr/Scripts/issues#4
isEndPoint(): Restrict 'roi-protection' to ROI-associated image
This ensures pruning of end-points above and below the ROI in
when the ROI is associated with a particular image in the stack
Extend 'roi-protection' mechanism to GUI
Enable 'roi-protection' mechanism in GUI only if appropriate.

By monitoring the presence of an active ROI, we make it
unambiguous for the user that the new option in the dialog
requires a ROI. If the user is recording a macro, disabled
option is not recorded to avoid unexpected surprises.
Make GUI more intuitive
- Organize prompt into sections
- Add Help button
Update javadocs
Merge pull request #2 from tferr/protective-roi

Create a pruning run() method that ignores end-points inside a ROI