Under Project Properties -> Project Facets -> Convert to faceted form... you can select Java - this will add the Java functionalities to your project. There you can also add other facets like Dynamic Web Module if necessary.
From what you have written the project was checked out correctly. The option Check out as a project configured using the New Project Wizard is applicable when the .project file does not exist in the repository and you have to select the project type manually. It will only create a new Eclipse project locally.
