Below are the most common problems encountered after updating a VM (although this may be equally applicable to source downloads).
You'll update, and none of the scripting will work. The Tools menu doens't do anything, and the browser throws a lot of Javascript errors. This is most likely because you made local changes to the Javascript files, but did not revert them before updating.
If you see any strings like "<<<<<<< .mine" in your Javascript file, this is the cause.
You may get an error like:
Parse error: syntax error, unexpected T_SR in /var/www/deki-hayes/includes/Attach.php on line 529
This indicates there is a conflicted file; when the update script tried to copy over the new Deki Wiki files, it found you made modifications to the same file. This most frequently happens if you applied a custom patch between release (which was then later issued in an official Deki Wiki release).
To correct this issue, go to /var/www/deki-hayes/ (or the folder of your Deki Wiki installation), and do a svn st. For every file that has a "C" next to it, you will need to (1) undo your patch, (2) update to the latest version of that file. If you wish to reapply your patch, you will need to do a svn diff -u filename before running these steps to know what changes you made!
To undo your local patch, run: "svn revert filename". To then update that file, do a "svn up filename"
These errors can manifest themselves in many ways; either with errors about columns or tables not existing, or missing stored procedures ("Parameter '?usernamefilter' not found in the collection.") This was most likely the result of the update database script failing. Attempt to run your database update again:
cd /var/www/deki-hayes/maintenance; php update-db.php
Take note of any error messages; if you get a "Could not connect to database"-like message, then ensure your root credentials for mySQL are correct in /AdminSettings.php.