Configuration files were migrated correctly. When I restarted tomcat and tried to log in XWiki, xwiki started a wizard. It downloaded the default XAR, and I saw an inverted triangle to the right of "CONTINUE" button. When I moved the mouse cursor over the triangle, I saw a drop-down menu with "INSTALL".
I thought "INSTALL" would install the default XAR, but when I clicked it, I saw the button replaced with a text saying "#execute..." or "#hold...."(I can't remember the exact text).
I guess this is something that looks like a bug ... By the way, is the distribution manager expected to pop up on an upgrade? I thought this should only happen on a fresh install.
From which XWiki version have you been upgrading?
I assumed xwiki failed to merge the new default XAR with the old XWiki. So I clicked "Skip" and continued migration process.
I'm not sure if database migration was successfully done because I failed to merge the new default XAR via the wizard.
I tried to import the new XAR, and I chose "Replace the document history with the history from the package" instead of "Add a new version to the existing document". That choice was ok except I had to uncheck some documents that contain information of user, right, and password.
Thus, the Main space WebHome was overwritten, and the admin password was reset to "admin".
When it comes to updating from a "relatively" old version of Xwiki, I prefer to do it "old style", i.e. import the *.xar manually, as you did. As you figured out it is better to exclude some pages, as listed in the http://platform.xwiki.org/xwiki/bin/view/AdminGuide/Upgrade#HUpgradingwikido... Additionally I think it is better to keep the "Add a new version to the existing document" checkbox checked, because just in case one forgot to exclude one of the pages one can recover from that mistake simply by revert to the version before the import. I am currently preparing a migration of a rather old (2.2) installation to 5.x, and as this installation has a lots of sub-wikis, it seems to pay off to manually create an "xwiki-subwiki-update.xar" which is the same as the xwiki-enterprise.xar except for excluding the Main,WebHome and the other pages which should be excluded anyway. However I am not sure how well that plays with the application manager for the next upgrade ... not too well, I guess, as it might think the "XWiki Enterprise UI" app is not properly installed. Cheers, Clemens