Running git pull returns an error to the effect: "Your local changes to the following files would be overwritten by merge.... Please commit your changes or stash them before you merge."

This is do to changes to the CRIkit2 directory on your computer that conflict with updates on the repo on Github. If you have not explicitly edited the repo, the most likely cause is (re-)building the documentation after you installed CRIkit2 via git clone

Simple solution.

cd CRIkit2 repo directory

# This will basically move your changes into an archive and set the install back to its normal state
git stash -m "Stashing changes"

git pull  # Now, do the update

This should fix the problem