you can create a new xtk:navTree in Navigation Hierarchy and add the list of needed items in the subfolders and name the root folder. you can add root which comes along with Database, web Application, Generic folders and you can add whatever subfolder you want to by mentioning in the newly created NavTree under Navigation Hierarchy. you might also have to add in Input forms if you have custom schemas included there.
It has been quite some time I did this work, so I cant add the screenshots. Do let me know if you need further help on this.