As long as the Protege server is happy to continue to run, you should be OK with that error message.
It looks to me like trouble with the installer.
When you download it, you should get a file called essentialinstall.jar (NOTE: not essentialinstall.zip). Once you've made sure that you have Java installed, you should run the 'essentialinstall.jar' file, which will take you through the installation process.
We have seen some problems downloading the 'essentialinstall.jar' file with Microsoft Internet Explorer, which insists on changing the file suffix to '.zip'. This is an issue with IE and downloading JAR files that is very tricky to consistently work around from the webserver end. However, all you need to do is make sure that this file is downloaded and saved as 'essentialinstall.jar'. I think you can do this when IE asks where you would like to save it but otherwise, you can simply rename it before you attempt to run it.
I'd like to get this possibly scenario out of the way, first - that the installer has not run correctly.
From what you've described, it sounds like you've received the installer as a '.zip' and when you double-clicked on it, Windows has unpacked the ZIP to give you the WAR file and the baseline repository Protege project that is in the, 'essential_metamodel.zip' file.
Apologies if you've already run the installer, been through the install wizard and all that. When it runs successfully, the installer will deploy that 'essential_viewer.war' file that you have to your Apache Tomcat (or other favourite Java Web Application Server) webapps folder. Also, the missing tab etc. will be deployed to your Protege plugins folder.
The other thing to note is that you must perform the install on the server that will host the repository and Essential Viewer. Additionally, the client components (Protege, Essential Widgets) must be installed on each workstation that you or your team will use to populate and update the repository. Users browsing Essential Viewer only require a web browser.
If you haven't already seen the installer running (
as per Section 5 of the multi-user install guide), re-name that 'essentialinstall.zip' to 'essentialinstall.jar' and double click on that.
Finally, assuming that the install has completed successfully, that error that you're seeing is related to the change-tracking set up. See Section 12
of the multi-user install guide and in particular the article on the
Enabling Collaboration for what's involved in setting up the change tracking and collaborative capabilities of Protege.
Let me know about how the install actually went and that you were taken through the install wizard.
Jonathan