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I’ve been seeing a lot of as-yet unexplainable “now it works–now it doesn’t” issues with a project. (It works on 8.10. Mostly it doesn’t on 9.04, except for a few days in June.) Just would like to rule out that any changes from updates are having an effect. Is there a way to tell which updates were applied when?
I’d take a look at /var/log/apt/term.log.. It’s a bit messy but you should find what you are looking for.
Edit: This will work as long as you use only apt (or one of its front-ends) for upgrading/installing packages (that is, as long as you don’t use dpkg directly)