Can someone explain how the organisation of classes in Pharo works in different versions of Pharo?
In addition there is SystemNavigation which somehow helps navigating classes and methods based on some of the above mentioned constructs?
Classes
The fact that classes are keys in the Smalltalk global is an implementation detail. As long as there is a single global namespace for class names, it is likely that the implementation will stay the same.
Class Categories
The class category is very much like a tag. A class can only be in one category at a time. Originally the class category was used by the Browser for organizing the classes in the system.
When Monticello was created, the class category was overloaded to also indicate membership in a Monticello package theMCPackage and PackageInfo classes were created to manage this mapping.
PackageInfo does all the heavy lifting: finding the classes and loose methods that belong to a package.
MCPackage is a Monticello-specific wrapper for PackageInfo that adds some protocol that wasn't necessarily appropriate for the more general PackageInfo.
Packages
Overloading the class category for package membership was a neat trick to ease the adoption of Monticello (existing development tools didn't need to be taught Monticello), however, it is still a trick. Not to mention the fact that the implementation of PackageInfo was not very efficient.
RPackage was created to address the performance problems of PackageInfo and to be used as part of the next generation of development tools.
Both package implementations will continue to exist until PackageInfo can be phased out.
SystemNavigation
As Frank says,
SystemNavigation is a class that, as its name suggests, permits easy querying of a number of different things: the classes in the image, senders-of, implementors-of, information about packages loaded in the image and so on.