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In the past I have tended to do a full install rather than an update when upgrading from one release of the OS to a later one. (E.g., Fedora12 -> Fedora13) I have done this (full install rather than update) since early attempts to use the update resulted in seriously broken systems.
The problem I have is that over the course of time, I add "stuff" to my system that is not part of a standard install, and after a full install, I have to 1)remember what I need, and 2)reinstall it. Or I have made changes to config files that need to be preserved across the system change. (E.g., the httpd configuration.)
Is there any way to ask the system "What have I installed beyond the 'standard' stuff?"? Or, alternatively, can I now expect an upgrade to work well?
As far as i know, upgrading and OS, does not interfere with custom applications, since the update system doesn't know about the existence in the first place. Secondly, it doesn't whipe the custom configuration done. It might mv the file to and .old file, and replace the current working configuration with the one from the upgrade. The reason is logical, if you think about it. Newer versions of applications, can have a change in features, thus configuration syntax. Some parts might become obsolete, or changed name. If you would not receive the new proper configuration file supplied, you would not know, and thus resulting in a malfunctioning application. (since your old configuration does not work on the new version).
You need to compare the configurations, and alter as needed.
It counts for all OS'es and supplied toolsets. (Solaris, BSD, Linux, Windows, MacOSX)
Some Distributions are made for being a rolling release, meaning on the fly upgrading (in a running environment), je some examples of these distro's are: Debian (and based on debian distro's), Slackware, Gentoo, Arch.. , other are not build with that method in mind, Fedora is such a distro. I don't say it cannot be done, but it's design is not, thus potential problem if doing so.
The safest way for Fedora to upgrade is using the upgrade mode, on the install cd set/dvd.
I can only tell you my preference, and that is to ALWAYS do a fresh install.
I've been bitten too many times in the past by an upgrade. While the OS does install cleanly (most of the time), I have found that you may be left with two (or more), versions of a library hanging around, different paths to the SAME library, etc. Causes all sorts of problems that are difficult to diagnose. A clean install, in my opinion, is always better. I usually install my all my software, databases, home directories, etc., on one drive/partition, and the actual OS on another. At install time, I can just format one partition, and keep everything else intact.
yes, correct, it's the safest (in some cases more work, since all apps need to be reinstalled/compiled/configured again). But the question (as i understood) was about upgrading, in relation to some problems, and what method of upgrading would be possible. (safe or not). And the why one needs to adjust things afterwards.