I have already developped a Java project using Eclipse. Now I would like to integrate an help system to allow the user to open a guide.
Browsing other questions i found this tutorial to set up Eclipse environment in order to use the Eclipse Help System. Anyway, this tutorial and all documentation I found since now, only explain how to use this system creating a new plugin project.
But what about if I want simply add the help system to an existing Java Project created in Eclipse IDE? Which step should I follow to update my project configuration? Is it possible to integrate Eclipse Help system, without using eclipse?
No, the help system you point to is an eclipse plugin based system, useful with RCP programs. See http://wiki.eclipse.org/RCP It will only run in the context of an RCP application.
You might be able to write an RCP app that contains only help, launch it, and communicate with it through http from your java app, but it's not a simple integration ... and you still have to build your help documents so that org.eclipse.ui.help can see them.