testMergeCheckout.sh

git init subRepo
cd subRepo/
touch a
git add a
git commit -m addA
cd ..

git init rootRepo
cd rootRepo/
touch b
git add b
git commit -m addB
git branch side
git submodule add ../subRepo/ sub
git commit -m addSub
git tag withSub
git reset --soft side
rm -fr sub
git checkout withSub
ls
## See how native git doesn't touch the filesystem because index==MERGE. If index==MERGE git thinks there is nothing to do.
## But JGit thinks the index has to be updated and therefore also populates the working tree.