Reproduction of work sometimes goes by the name "provenance." 1. Record what you want to do. 2. Record how, when, where, by whom it was done. 3. Include ability to run it again. (Exact reproduction is understood to be impossible given everything that can vary in the hardware, OS, and software.) There is an encoding format for provenance, called Open Provenance Model, that can function as a guideline for how to record actions faithfully.
A good example is VisTrails, a workflow application. If you use it to make an image, then you can click on that figure in a PDF, and the URL leads to an online record of what made the image, which downloads to your local machine and runs. You can pick up where the author left off (software, data, internet permitting). Running every program under such a workflow is cumbersome or impossible, though, but it's work in the right direction.
A good example is VisTrails, a workflow application. If you use it to make an image, then you can click on that figure in a PDF, and the URL leads to an online record of what made the image, which downloads to your local machine and runs. You can pick up where the author left off (software, data, internet permitting). Running every program under such a workflow is cumbersome or impossible, though, but it's work in the right direction.