Flashing and Programming
On a hosted system, "running the program" means handing a file to a loader. Here it means writing your image into non-volatile memory inside the chip and then resetting it, using a second piece of hardware that talks to the silicon over a two-wire debug port. That second piece of hardware is doing considerably more than copying bytes: it halts the core, drives the flash controller through a sequence the reference manual specifies, verifies, and releases reset.