I'm entering this to generate some discussion before deciding whether or not (and how) to proceed.

If the user has the save confirmation dialog enabled, it will also pop up when a save is triggered by the CLI command processor (either directly from the CLI or from a running command script).  This can (unexpectedly) halt the command processing, requiring manual intervention by the user in order to continue.  Should the confirmation dialog be disabled for save actions initiated by the command processor, or should there be (yet another) option setting to determine if the dialog is show in this case?  Rather than adding another option, perhaps the existing save confirmation setting could be converted to a set of radio buttons or checkboxes (or combobox) to select the desired action.

See the follow up comment below.