MEDIUM: patterns: reorganize pattern reference elements

MEDIUM: patterns: reorganize pattern reference elements

Instead of a global list (and tree) of pattern reference elements, we
now have an intermediate pat_ref_gen structure and store the elements in
those. This simplifies the logic of some operations such as commit and
clear, and improves performance in some cases - numbers to be provided
in a subsequent commit after one important optimization is added.

A lot of the changes are due to adding an extra level of indirection,
changing many cases where we iterate over all elements to an outer loop
iterating over the generation and an inner one iterating over the
elements of the current generation. It is therefore easier to read this
patch using 'git diff -w'.