If you have ever cut or drilled into steel you should have noticed some burrs and tool marks. A little sandpaper and it is usually easy to make it smooth to the touch and the eye. Making a rifle barrel is no different, though the scale is. The cutting of rifling and the chamber can leave tool marks. Maybe they are not seen with the naked eye, but they are almost always there on a new barrel. Hand lapping gets rid of most or all of them from the bore, but not all rifles are hand lapped.
Additionally there are almost always tool marks left in the chamber throat. The throat may be a tiny part of the barrel, but just like the crown, it has a huge effect on accuracy. Generally speaking, a shot out barrel is simply a barrel with a chamber that is worn out.
Breaking in is simply using fired rounds to smooth out any tool marks. It just needs to be done with a degree of care to prevent copper build up. Depending on the barrel, the tools used to make it and the processes used, whether it is lapped or not and so on can affect if you need to clean out all copper between every shot for the first 1, 5 or 25 rounds or if you can get away with firing 20 rounds and then cleaning out the copper. So what should you do?
Well, nobody knows what tool marks are left better than the people that make them, so my advice is to follow whatever the barrel maker recommends. Below are links to a few different ways makers suggest to break in your barrel. Everyone agrees if you have your own way, use it. Just listen to what the barrel tells you by watching the patches and be patient.