Org-mode [1], actually; it has various mechanisms for embedding source code fragments in documents. The fragments can be evaluated when exporting to PDF, for in

Org-mode [1], actually; it has various mechanisms for embedding source code fragments in documents. The fragments can be evaluated when exporting to PDF, for instance; listed; or "tangled" (extracted) and compiled. My projects usually evolve from a TODO file with source-code fragments for subproblems; then, by a process of conjugation, the fragments are tangled into viable products. The TODO captures the evolution of the project, and follows the trajectory of eventually accepted or rejected ideas. [1] http://orgmode.org/guide/Working-With-Source-Code.html http://orgmode.org/guide/Working-With-Source-Code.html