1. We need a unique constraint before the foreign key...

ALTER TABLE grouper_stems ADD CONSTRAINT grouper_stems_id_index_unq unique (id_index);  

2. You can wait until next release and it will "just work"
3. If you want to just do the manual DDL and set the upgrade task to complete that is what I recommend
3a. Get the oracle parts from the source (and if foreign key fails add that constraint above and let me know)
https://github.com/Internet2/grouper/blob/GROUPER_6_BRANCH/grouper/src/grouper/edu/internet2/middleware/grouper/app/upgradeTasks/UpgradeTaskV37.java
4a. You can set upgrade tasks to not run or fail on startup (see 4d)
4b. You can assign the 37 attribute to the group of upgrade tasks to tell grouper its done (see 4d)
4c. undo 4a setting upgrade tasks to not run, and it should fail on startup (see 4d)
4d. https://spaces.at.internet2.edu/spaces/Grouper/pages/318572008/Grouper+upgrade+tasks#Grouperupgradetasks-Skipanupgradetask (edited)