Approaches for linking form instance changes to individuals

Very thorough options! I'm going to absorb these options for a bit, but wanted to quickly point out that when reading this, I'm realizing OpenClinica (clinical trial software) has built something very similar on top of Enketo (i.e. ODK XForms). Audit trail, comments, reason-for-change (and a lot more). There is some magic involved, and the form format extensions we used would not pass muster for our generic specification (stored as stringified JSON in a single XML node per question), but maybe some elements are of use. It is built on top of a basic comment feature in Enketo, which I think would pass muster spec-wise (I didn't get it into the ODK spec though tried). FYI, see this XLSForm (it can be tested on http://opendatakit.org/xlsform/)

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