A programmer on my project is going to leave in about a month. We stress the principles of A Quick Guide to Organizing Computational Biology Projects (disclaimer: written by this lab's principal investigator). I've stressed the importance of version control before, and he reports that major application code is all in version control, and run scripts are all in dated directories, such that it should be easy to find the script used to create a particular file in his dated lab notebook by looking at the surrounding dates.
His code is well-written and I haven't had much trouble figuring out how it works when I need to. My biggest concern is finding the right file. All the version-controlled application scripts should be described by a line in a README file, and I think I'll probably try to make do with figuring out where lab notebook files came from using the date and by grepping the name of the created files.
I also don't want him to spend too much time documenting when that is always imperfect and he could be working on new code or fixing bugs instead.
Are there any suggestions or things we didn't think of? Things you wish you had asked of programmers before they left your lab?