Absolutely... here ya go:
Note, too, that hovering over the other menu choices near "Cover Art" correctly show FireFox pointing to the other .jsp files that do exist as well.
Now, clicking that Cover Art link results in this:
And that's what makes no sense. However in 4.1, that coverArtSettings.jsp file does exist --- if it was removed in 4.4, then it seems illogical that the Cover Art link up top would still point to it.
Lastly, here's the Search box failure:
As for the WAR deployment, definitely not manually deploying. The way I'm deploying is downloading the latest war zip file from SS site, unzipping it in my home directory, and then copying the .WAR file into $SUBSONIC_HOME/webapps. When I do a "service tomcat6 start", Tomcat automatically deploys that WAR file and creates the "subsonic" directory and subdirs. That's how I deployed the 4.4 version of the screenshots above.
The system reboot was purely a one-off, first time I'd done it. Generally (as with most things Linux) a simple service restart will suffice (service foo restart, for sysV flavours).
As for the cleanup -- all old versions of Subsonic are completely gone from $SUBSONIC_HOME. I have not yet, however, touched anything in /var/subsonic --- but I will give that a shot now, particularly the "subsonic.lck" suggestion you just made.
Question, however: when you hover over the "Cover Art" link in that upper menu under Settings.... what does your browser show as the destination URL, for 4.4? is it "coverArt.jsp"?