Outline A efficiently presents a large body of material, and is good for reference usage. In the Outline B, the commands are presented in the order that the user needs them when first learning about the system. This is primarily a tutorial organization that is aimed at first-time, novice users. Tutorial manuals tend to be longer and less useful as a reference guide. In either case, the Introduction should make explicit the knowledge expected of the reader, and you might specify where to obtain the required knowledge by referring to the appropriate texts or reference manuals.
Many products come with a small tutorial manual and a separate, thicker reference manual.
Products with many commands that must be frequently used often include a Reference Card that can be overlaid on a keyboard or a template that can be taped on a data tablet. Another property of the user manual organizations above is that they explain the system in stages with increasing detail. Even if the reader wants a complete understanding of the internal workings of the system, this zoom feature is important to help the reader maintain perspective on how the details fit together into the overall system. Remember, it's often best to sneak up on the Truth. One of the implicit goals of a user manual is to help the user to build a conceptual model of the system.