My company is developing guidelines for employees to document their work so that in the event of an external audit there is a clear trail of what was done. So, just as bench scientists fill in their lab notebooks, we bioinformatics folks are expected to record our work in a "notebook". The question is: what is exactly worth documenting? Should every minor change in a script be recorded? Or should a written summary of what tasks a given program accomplishes suffice? I would like to hear about your experiences in documenting your programming/data analysis work.
To keep track of the chronology of the bash script / README, the "obvious" solution would be to put them under version control as well. Even if you don't keep good commit messages, it'll help to track down "when did I decide to change parameter X?"
I'm still working out my methodology, but when in doubt I make a fresh repository for every project and check everything I write into it.
+1 you're right. I should start using a version control system for the bash script and README files :-)
about the chronology, you can add "map de !!date<cr>" in your .vimrc. Then you can type d e in the vi to insert the data.