Add constraints upgrade task is very slow in instances with a large amount of users

Summary

Upgrade hangs on EmbeddedCrowdAddMissingConstraintsClearDataUpgradeTask when upgrading to 5.10 or above

Steps to Reproduce

1. Connect Confluence 5.9 or below to LDAP to pull 50k+ users
2. Run the upgrade past 5.10

Expected Results

Upgrade completes as expected

Actual Results

The upgrade hangs on:

2017-04-25 18:16:09,646 INFO [localhost-startStop-1] [atlassian.confluence.upgrade.UpgradeTask] doUpgrade UnindexContentTypeUpgradeTask for status
2017-04-25 18:16:09,653 INFO [localhost-startStop-1] [atlassian.confluence.upgrade.UpgradeTask] doUpgrade UnindexContentTypeTask enqueued

Notes

The query that it hangs on is the following:

SELECT DISTINCT membership.id as id1_29_0_, membership.parent_id as parent_i2_29_0_, membership.child_group_id as child_gr3_29_0_, membership.child_user_id as child_us4_29_0_ 
FROM cwd_membership membership, cwd_membership mem2 
WHERE (membership.id <> mem2.id 
       AND membership.parent_id = mem2.parent_id 
       AND (membership.child_user_id = mem2.child_user_id 
       OR membership.child_group_id = mem2.child_group_id));

For instances with very large user bases, this takes a long time to complete.

Workaround

1. Delete the external directory that has all of these users from -> General configuration -> User directories
2. Run the upgrade
3. Re-add the directory connector
   This is not recommended if you have an external directory set as 'Read only with local groups', as these memberships will be lost
   OR
4. Wait for the upgrade to complete, it will just take longer than usual