The core of MorphOS is compressed and stored inside a boot.img file which must reside on some storage medium accessible by the HAL/OF. This file is loaded by the HAL/OF and starts up the Quark microkernel, as well as a number of other low-level basic components of the OS. The rest of the OS is formed by hard disk based files and runs on top of this software layer.
Amiga was characterized by advanced low-level software features provided by its microkernel, Exec, like pre-emptive multitasking, inter-process communication, etc., that were absent in any popular computer of the late 80s (early Macs and PCs, Atari computers, etc.). Of course all these features are provided in MorphOS by Quark, which is also able to support more modern features like memory protection, virtual memory, and so on. Quark is also able to provide a number of sandboxes where virtualized operating systems can run independently. Currently two sandboxes are implemented: QBox, which now is used for low-level processes only, and ABox, which provides a special API for programs and applications. Indeed this API is fully compatible with AmigaOS 3.1 (the last operating system created and distributed by Commodore for its Amiga computers) and, together with Trance, a JIT emulator for Amiga executables, guarantees a high degree of compatibility with the large set of Amiga legacy applications.
Note that the huge number of excellent games that made the Amiga famous in the late 80's and early 90's do not run directly in MorphOS environment. Amiga computers were equipped with custom chips for graphics and audio. Their operation is totally incompatible with a modern system like MorphOS, which is able to manage current 2D/3D GFX boards and on-board or PCI-board audio. If you want to play old games on a Pegasos/ODW, you can, but you need UAE (the Universal Amiga Emulator), which is also available for MorphOS and provides the required compatibility.
The native compatibility of MorphOS with Amiga legacy software, instead, has a different target. Users can run almost all the most recent and advanced Amiga applications, which are able to manage additional GFX and audio boards created for the latest Amiga computers. The relevant software layers, known as CGX (CyberGraphX) and AHI (Audio Hardware Interface), mask and manage the re-targetable hardware and are fully integrated in MorphOS.
Like the AmigaOS, MorphOS makes two very compact, efficient, and fully integrated interfaces available (Command Line Interface and Graphic User Interface) for shells and applications. Although this "built-in" CLI/GUI system can easily get the job done, many prefer significantly more advanced features and "eye-candy" in the GUI. To address this, MorphOS has adopted the more object-oriented software GUI layer called Magic User Interface. MUI not only provides the programmer with more sophisticated GUI interactions and layouts, but also allows users to more fully customize these GUIs to their individual tastes. Actually MUI is one of the most distinctive components of MorphOS, both in terms of features and aesthetics.
MorphOS shell is a Unix-like shell provided with all the features you expect from such a component: AmigaDOS commands (most of which are Unix-like), local and global variables, command substitution, command redirection, named and unnamed pipes, history, programmable menus, multiple shells in a window, ANSI compatibility, color selection, and so on. Of course the set of commands includes all the necessary commands for scripting. In conclusion: Command Line Interface users will not be disappointed...
Ambient is the MUI based, fully asynchronous, multi-threaded, default native desktop of MorphOS. Although open sourced, in practice Ambient is an exclusive component of MorphOS, because it is so strictly related to MUI and the OS that its porting to any other environment would be very difficult. Ambient provides program icon management, directory navigation, program launching, file handling, and everything needed for managing the system. Ambient is highly adaptable to the user's taste: file management can be done in classic (spatial) mode or browser mode, using icon view or list view. Filetype recognition is done by means of direct file probing and/or mimetypes, and users have full control and editing capabilities on mimetypes for a fine-tuning of the related actions. Ambient allows the user to easily perform any type of activity with the built-in tools: file search utility, text viewer, picture viewer, sound player, system monitor, disk formatting utility, management of commodity utilities, and much more. From Ambient menus, users can control all the settings in their MorphOS environment, including MUI settings and the desktop itself.
Let me mention in passing that users are not necessarily forced to use Ambient. Other common desktop environments of the Amiga world can be run at the same time, or even as complete substitutes for Ambient, e.g. Directory Opus (also available for PC users as a substitute for Windows Explorer), Scalos, and even the classic Amiga Workbench (but this is reserved for crazy users which like some hacking).
The previous components of the OS are those that the user always sees and manipulates: their visual impact and easy handling have a high influence on user appreciation. Ambient users, for instance, can select distinct skins, changing on the fly the general aspect of all the windows, widgets, and other graphic elements of the desktop (some distinct skins are shown in the pictures). On the other hand, other system software runs invisibly and silently, but is equally important, because without it the computer will be unusable. A few examples are filesystems, USB management, printer drivers, advanced scripting systems, etc.. Of course all these components are present in MorphOS, but only short descriptions are given here, mostly concerning special features that adds to those that users automatically expect from this hidden software.