Mary, we've been using the nested folders of outcomes, too, so that they can easily be embedded in any assignment rubric without totaling the assessment criteria points. So far, it's been working great, as long as faculty remember to "uncheck the box" for points totaling when they add the criteria to their rubrics. I say that phrase a lot in trainings!
The only difference in what we did -- at Canvas' excellent advice -- was to code our assessment criteria and its associated folders. We have both university-wide and program-specific assessment that we are managing all at once, and the coding has made both the available folder structure in any given course site and the CSV report much more clear.
For example, we use the AAC&U "VALUE" rubrics for undergraduate general education assessment, while our Art Therapy Counseling program has a specialized accreditor called CAAHEP that has provided us with outcomes criteria.
So, if I'm looking at a report, a code of MU.VALUE.IL.C1 tells me that I'm looking at campus wide (MU), VALUE criteria, the Integrative Learning rubric (IL), and criteria one on that rubric (C1).
Contrast that with ATC.CAAHEP.SLO.A tells me that I'm looking at the Art Therapy Counseling department (ATC), CAAHEP criteria, a student learning outcome (SLO), criteria A (A).
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