The following has been used for this:
git grep '^CREATE' tests/queries/**.reference | cut -d: -f1 | sort -u | xargs -n1 -i sh -c 'show-create-rewrite.py < {} | sponge {}'
show-create-rewrite.py is available here:
https://gist.github.com/azat/916b98b5ddf9573f7dc9a4dce33b59b5
And for 00998_constraints_all_tables test FORMAT TSVRaw I simply drop.