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In reference to issue #1509, I wrote an implementation of the Transformer plugins as described in that issue and implemented in https://github.com/PeteMichaud/jekyllpedia/blob/master/_plugins/jekyllpedia.rb (Note: the jekyllpedia thing is only meant as an API reference, the implementation is broken in like 6 ways that I can see off the top of my head, don't use it until I actually write it correctly).
I opted to Transform prior to the liquid conversion (see https://github.com/PeteMichaud/jekyll/compare/transformer#L1R139), because I thought that was probably more powerful than the other way around. Now Transformers can potentially inject or alter the liquid code before that code is rendered to a final page.