Keep code and developer documentation in the visioneval code tree

[jrawbits]

Documentation that may be upset by changes in the code tree needs to be maintained in the code tree.

That means creating R code (executed by .Rmd when the book is rendered, but probably also pre-populated through a build function that knows about the documentation book specifically) that will pull out module_docs, input file descriptive information, model estimation information, etc.

Each package and module should have better-structured documentation that gets sucked up into detailed, well-linked appendices in the documentation book.