I have been using several Linux distros for about 20 years, and Linux as my main laptop OS for about 10. Several times, after installing software (notably different python or perl versions) or upgrading (apt-get upgrade) I run into incompatibility issues and instabilities which some times led me to reinstall the system afresh. I currently use Lubuntu (LTS version), and various Virtual Machines / Docker Containers to keep my critical applications running independently of my base system.

Is there any accepted best practice about how to keep a properly functioning system for long term use, while having access to the latest version of installed software?

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    Yes, kind of, I run the upgrade every day. Never had an issue. – LinuxSecurityFreak Mar 12 at 11:56
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    Set up an system with identical configuration and update that as a test before updating your "production system". Also, minimize personal tweaks to the default configuration. – Kusalananda Mar 12 at 12:29
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    You have not been clear about the problems that you experience. However only install from the distros repo, using the distros installer, Or into: users home directory; /opt; or /usr/local. – ctrl-alt-delor Mar 14 at 22:20

Maybe you're looking for something like Fedora Silverblue? It's supposedly installing/managing packages in a similar way to flatpack, but for the entire OS. This should allow you to keep your packages running in a certain version with all the right dependencies (or multiple ones at the same time). Only drawback here is that you'll need slightly more diskspace.

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