Hi Andrea,
You're right actually, that is a strange omission.
There is a way to set title, links, dates, etc for BundleEntries but it isn't obvious. There is a
getTitle() method which returns a StringDt instance which you can then set the value of.
E.g.
nextEntry.getTitle().setValue("This is the title");
..but I think we should also add a normal setter, since using a getter to set a value is pretty counterintuitive. Seeting links is a bit more intuitive:
nextEntry.setLinkSearch(new StringDt("
http://foo"));
And (hopefully I'm understanding your second question correctly) using top level resources in a bundle as opposed to contained resources is the preferred mechanism in FHIR. Contained are allowed for when a resource doesn't have its own discrete identity but in general using top level resources is the right way to go.
Cheers,
James