I am using eclipse 4 application platform for building custom ide like app, but i am still not sure what libraries i can use.
For instance i can't find some API which is responsible for maintaining projects. Is it even possible to create project or this is just part specific for eclipse as IDE and can't be used if i am using e4 rcp?
The org.eclipse.e4.rcp, org.eclipse.emf.core and org.eclipse.emf.ecore Eclipse features list all the plugins that a pure e4 application uses.
The list includes most of the org.eclipse.core.xxx plugins but not the org.eclipse.core.resources plugin which contains the workspace code (things like IFile and IWorkspace).
So if you want projects and workspaces you would have to write you own code for that - which would not be compatible with any other Eclipse 3.x plugins.