My tool takes the approach of more of a literate-project approach where one file may generate multiple files (and multiple files could generate one file). The idea is that the organization is completely up to the author with no boundaries between how they want to organize it.

And referring to earlier comment, I would write the same flow of logic for a single thought in the same place. There is the flow of a single process and there are commonalities across processes. I think a good literate programming allows the uniqueness of a single flow to be put into one place and the commonalities to be extracted and applies to such a flow.