When running a pogram with the '-save' argument, the history should be saved regardless if HistoryRecording is turned off in Preferences
Currently, if you run an ISIS program from the command line with the '-save' argument (see the isis3 documentation for information on command-line usage), the history will not be saved if, in your IsisPreferences, HistoryRecording is turned off. When '-save' is used, this should override the preferences. I believe that this behavior is happening in the method SaveHistory() in UserInterface. In this method, we check to see if HistoryRecording is turned off, and if it is, return. We should be checking if 'save' was used before the preferences.