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If I simply upgrade the Linux I'm using, is there anything that doesn't really upgrade until I install the OS from scratch on a new partition? Or can I unworryingly upgrade from the terminal without fear of ending up outdated?

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No. In most cases, it's even the other way round. At the time a version of a Linux distribution is considered stable and released (e.g. "Ubuntu 11.10"), many packages will already be outdated again.

You can try this with almost any fixed-release distribution. Get the latest installer and check it for updates after installing. Chances are you'll already find new software packages. With rolling-release distributions, it's the exact opposite. Here, there's no special release version. You'll always get the latest packages when installing. For example, Arch Linux uses this model.

Arch Linux releases are merely a snapshot of the /core repository, combined with various features or modifications to the installer script itself. The rolling release model keeps every Arch Linux system current and on the bleeding edge by issuing one command.

So, if you have a typical fixed-release distro, the safest and easiest way to stay up-to-date is to just keep using the version of your distribution you currently have and regularly update your packages – with yum, apt, or what have you – until it's considered EOL ("end of life") and doesn't get any future security updates.

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Yes, sometimes you can have issues with upgrading. In fact, one thing I have learned over the past ten years is that I would prefer to do fresh install every time instead of upgrading. Two reasons:

  • Many apps try to adapt themselves to old settings of the previous version. Sometimes, this is not what you want. Some years back, when Gnome 2 moved to a new menu layout, it was shown only to people with fresh installs. Gnome didn't want to suddenly change the menu layout for users who have previously customized their menus. While that was a polite thing to do, I missed out the new layout completely because I had done an upgrade. I had to wipe out the gnome configuration to get the new look.

  • Because of the literally infinite permutations and combinations of previous settings out there in the world, new distro releases cannot obviously do a complete job of QA for upgrades. At the very minimum, they do a good QA for fresh installs. But for upgrades, they need to think up of various states of previous releases to test on. And they could only do a few possibilities. Beyond that they completely rely on other users trying out upgrades on their systems hoping to catch some corner case that they didn't think of earlier. The chances are, that you might encounter a corner case problem that is almost impossible to debug because of the unique setup that you have in place.

It is a bit of a hassle to backup settings before wiping out the disk for a new install and restore later, but try it a few times, and you will think up a system for yourself that you can follow blindly. Like keeping all your data in only one or two places, only needing up to backup /etc and /home, etc.

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