Sidehistorik
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For some customers we have added the App Extended Schemes for Jira, wich give the ability to (amon other functions) to control wich links can be usesed for issue types (Link Scheme).
Changing peoples process
Im sure that removing or disabling subtasks can cause fustration for hardcore and experiend users of Jira, so do always remember to argument and educate for the solutions You implement. Its all a matter of the way people work and are educated to use Jira ....