Hi. About the SMath messages, the style "in your face" is a little angry. Even more when actually those messages are only warnings, not critical errors or something "important" thing. For plugin's updates, I guess that it's enough the status bar with a warning abut that the update was effective only after restart the program. And when open a file done in a newest version than the user have, or open a file with plugins that the user don't have installed, proceed with open the file, but disable autoeval by default for those both cases, and open the file, with a warning message in the status bar.
About the SMath instances, double clicking a file in the file explorer open that file in a new SMath instance, but not in the running, if there is one. ¿Can this behavior be modified by a global option in the SMath configuration?
Best regards.
Alvaro