Literate programming tools should never enforce that the code in the woven (pdf/html output) view appear in the same order as it does in the original code view. Unfortunately, Alectryon requires definition-order documents. I would much prefer something like Torii where I can weave the code together in an order that makes pedagogical sense, but does not necessarily pass the proof checker. The writing style in this document is severely hampered by the need to present everything before it appears.
This is the biggest issue in most literate programming systems in my opinion. Also having read some books/content that have been generated from literate programming tools you can "feel" the authors being limited by the form of the tools. Also examples which don't typecheck/run are clearly inferior/second class. You really need something that feels more like transclusions and does not require the text to be the exclusive source of truth.