Upgrading from previous versions older than 2.5.0:
The upgrade scripts from older versions to 2.5.3 are not complete, however it won't affect your XOOPS site. The scripts will be improved in next release.

Following is an instruction for upgrading from XOOPS 2.4.5 to 2.5 provided by John Healy:
0. Verify the system requirements, in particular the version of PHP. Backup your XOOPS database and site directory. (There are several ways to do these actions, which are discussed elsewhere.) Turning your site off is optional.
Change the permissions on mainfile.php and /include/license.php to be writable, for example:
File Normal For upgrade
mainfile.php 400 700
/include/license.php 444 777
Get the correct update package from the SourceForge file repository.
1. In the upgrade package folder, move the "upgrade" folder inside the "htdocs" folder, if it's not already there. Remove the install folder from the "htdocs" folder, if it's there. Remove the mainfile.php file from the "htdocs" folder, if it's there.
If you've moved the xoops_data and xoops_lib folders outside your site's root directory, move these folders out of the "htdocs" folder in the upgrade package folder.
2. Delete the /modules/system directory on your current XOOPS site (to get rid of any old unnecessary files).
3. Overwrite the files in the XOOPS directory on your current XOOPS site with the content of "htdocs" folder of the upgrade package. (There are several ways to do this action, which are discussed elsewhere.)
As noted above, if relocated, overwrite the files in your current xoops_data and xoops_lib with the content of those in the upgrade package.
4. If you have Protector previously installed, open the "mainfile.php" file , and remove the Pre-check and Post-check lines (if they exist):
include XOOPS_TRUST_PATH.'/modules/protector/include/precheck.inc.php' ;
include XOOPS_TRUST_PATH.'/modules/protector/include/postcheck.inc.php' ;
5. At your site's address (URL), login as administrator. Access <your.site.url>/upgrade/ with a browser, and follow the instructions (and any for updating your XOOPS database). After all updates have been applied (green checkmarks), note the link in the Updater to update the "system" module, and do so.
6. Delete the "upgrade" folder from your site's "htdocs" directory.
7. Update (reload) other modules, especially "Profile", "PM", and "Protector," if necessary.
8. Change permissions on the files noted above back to their normal state.
9. Turn your site back on, if you turned it off earlier.