add "developer notes"

[gregcaporaso]

I think it would make sense to highlight some of the discussions that are included as Developer notes, where we briefly describe things that you'd want to think about if you were developing the functionality described in the text. These could be highlighted in some kind of box to stand out from the rest of the text. An example is in the pairwise alignment chapter:

Next steps: All of those steps are a bit ugly, so as a developer you'd want to make this functionality generally accessible to users. To do that, you'd want to define a function that takes all of the necessary input and provides the aligned sequences and the score as output, without requiring the user to make several function calls. What are the required inputs? What steps would this function need to perform?