Before talking much more about embedded programming, this is a good place to give a brief overview of how an embedded program starts up and runs. Assuming that you have generated a program file and have loaded it into the μC program memory (all steps that we will talk about in more detail later), the good stuff happens when you either turn on the device or you push the RESET button. When the μC comes out of reset from either action it will always go to a particular memory location, as defined by the manufacturer, to begin executing whatever code is found there, or pointed to there. Sometimes this memory location contains code directly; e.g. upon coming out of reset, program execution begins at program address 0. Other times the fixed memory location is a vector, a location that holds the actual address of the beginning of the program; e.g. upon coming out of reset, the controller will load its program counter with the value found at program address 0xFFFE and thus start executing code at the address found in locations 0xFFFE and 0xFFFF (assuming a 16-bit program address, stored in 2 bytes). In the first instance you will have to make sure that your program has loaded at the specified startup address, while in the second instance you will load your program wherever the program memory has been placed in the controller address space, and you will have to make sure that you then load that startup address into the reset address vector. Note that the choice of startup method is not up to you, but will be built in to the design of the μC you have chosen. AVR uses the first method, and Cortex M3 uses the second.
When an embedded program starts to run, there is usually a fair amount of initialization and housekeeping that must be done before the meat of the program begins. Most of this initialization is something that the average desktop programmer never sees, since it is handled by the computer boot code and operating system. But in an embedded system, it is just as likely as not that there is no operating system, and all boot code and other startup code must be explicitly provided. Some very critical hardware may need to be initialized first e.g. hardware that controls memory access times and address maps, as well as system clock hardware. Then some software initialization may need to happen, such as setting up a stack pointer and perhaps copying data from nonvolatile memory to volatile memory where it can be accessed and perhaps modified. After that will usually come another round of hardware initialization, setting up any peripheral devices that the system requires, and setting initial output states. Finally, yet another round of software initialization may occur.
This initialization is usually broken up into two sections, with the first hardware and software initialization steps often being done in what is known as the startup code, and the later hardware and software steps being done in the user program. This delineation is more distinct in a C program, where the startup code is invisible to the C program, being the code that happens before main() is run, and ending in a jump or call to main() where the visible C program begins. In an assembler program all the initialization steps may be equally visible in the user code, although even then the first steps may reside in a separate startup source file.
Each tutorial section will include a number of short example programs. The examples will start with the simplest concepts and add some concepts in each succeeding program. Along the way, some comments will be trimmed to try and help keep the visual clutter down and keep the focus on the newer concepts being presented. As an example, comments to the effect that "this bit/port/address needs to be adjusted for your particular hardware" will eventually disappear, because by then you should know that e.g. if I am discussing an LED output on PORTA bit 0 and on your hardware you are using an LED on PORTB bit 7 then you'll make that change accordingly. Or when I mention in the first programs that after a "ret" instruction that you'd better have set up the stack first, after a while that comment and others like it will disappear.