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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'.