OK managed to install Essential Project for multi user configuration.
The documentation is well done.
There are just a couple of things missing so here are some notes on the installation should someone hit the same walls.
The installation environment is Ubuntu 8.10, Protege 3.4, Java 1.6, MySQL 5.0
All went correctly up to the metamodel editing.
Before doing anything and especially before converting it to a Database format make a backup copy of the metamodel files, since if something goes wrong you will not be able to recover a working protege_server.
First you need to create the annotations file for collaborative work.
These files do not come with the downloaded zip and you can generate them using protege:
Just open the essential_baseline_v1.pprj with protege and in the Collaboration menu choose "Show collaboration panel" leave the default option to create the annotation files anew and you will be proposed correct nemes for the annotation file (it will be created in the same folder unless you decide to change it).
Also you have to create also GroupOperation for Viewer and Architects so that they can DisplayInProjectList and give to the repository you create in the 8.2 step of the documentation also this role (otherwise you will not be able to see it and choose it once you connect to the server).
The annotation project the documentation ask to define will map to the files created before.
This annotation project should not be displayed in the project list so do not apply that rule on it.
Ok now is installed time to use it ...