Merge pull request #4074 from RosettaCommons/roccomoretti/crash_display_change
Adjust the application signature for new crash reporter scheme.
The crash reporter PR (#2978) introduces a slight change in how exceptions should be handled in executables. Instead of the application displaying the message itself, it should call the Exception::display() function, which will handle doing the appropriate display (and any applicable crash report generation).
Most of this is just somewhat mechanical changes to the source/src/apps files. (I've also updated the code templates) But I also have changes to the JD2 & JD3 exception handling, such that errors which are caught by the JD machinery will also generate the appropriate logs.