For upgrading a pre-2.x SP version, see the NativeSPUpgradeOlder topic.
While the reinstallation process should preserve your configuration and log files, it's a good idea to save these files just in case, by copying your etc and var/log folders to a safe location.
Beginning with V2.5.0, the installer is now "servicable" and supports in-place upgrades for patch, minor, and major releases. Run the latest installer and your system should be upgraded. Of course, saving your older configuration files is always recommended just in case.
To use the new installers, the previous installer has to be removed first. In most cases, the new installer will detect this if you forget, and warn you about it.
1. To remove the older software, you should begin by stopping your web server, and then access the Add/Remove Programs feature in Windows and perform a "Change" operation. The "Change" option should give you the option to "Remove" the software at that point.
Do NOT attempt to directly "Uninstall" the package, or it will hang (this bug was the reason older versions didn't handle upgrades properly). Instead, follow the directions above. "Change" followed by removal should complete successfully. Newer installed versions explicitly disable the Uninstall option, but the older releases did not.
At this point, the software files will have been removed, but your configuration and log files will be intact.
2. You generally don't need to reboot at this point, and can proceed directly to reinstall the software using the newer installer. Be sure to select the same installation directory and other options that you used originally. If you fail to do so, your old configuration will not be adopted by the new installation without manually copying and/or modifying files.
3. Assuming you follow these directions, when reinstallation completes you should be able to immediately restart the upgraded Shibboleth Daemon Service using the Services administration tool. It should be using the same configuration as before (check the log file to ensure it appears to be running).
4. For a non-IIS installation, you can then proceed to restart your web server at this point, and service should be restored using the new software. An IIS server MAY require manual intervention to recreate non-standard filter and script mapping rules in some cases. You may want to examine the IIS configuration and check for the Shibboleth filter and ".sso" script mapping in the places you expect to find it before attempting to restart the IIS service.
5. Once you've verified your system is working properly, you'll want to remove the backup of your configuration files (since it probably contains your private key).
6. Finally, when time permits, you'll want to check the NativeSPReleaseNotes topic to see if there are any configuration changes required to bring your system fully up to date. All compatible upgrades are guaranteed to maintain the integrity and "correctness" of your existing configuration, but you may be left with deprecated settings that could eventually cause problems or prevent new features from working.