I'm looking at app development for ubuntu phone and it really looks great! But is it possible to access the native functionality of the phone like make a phone call or save a file?
The API documentation does only cover UI elements.
The documentation says that Qt5 and HTML5 are the technologies to play with. Qt has extensive APIs dealing with every kind of "native" (non-web) functionality. Well, they are native apps with not that much of restrictions. In the case of HTML Apps there is nothing published but the web standards themselves. But both, Qt and Js in HTML, have some file access API for example.
I asked a more specific question regarding also phone calls and the like: What is the equivalent to Android Intent and BroadcastReceiver?