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Ubuntu's update system maintains new minor versions of the current version branch but it doesn't update it to a new version branches. For example in Ubuntu 10.4 I have Evolution 2.28.1. That was updated to 2.28.2 and to 2.28.3 for now. But there's already 2.30.3 version on official site.

So my question is how do I update my apps to a new version branch replacing an older version of the app and keeping up Ubuntu's features like updating to a new minor version of the current branch?

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Look up the program name on Google to find its launchpad PPA and add that to your list with the instructions it provides.

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