We need to move data from the "active_list" and "active_list_allergy" tables to the "allergy" and "allergy_reaction" tables.
This could be accomplished by a couple of a changesets in the file "liquibase-update-to-latest.xml".
Take a look at example changesets in this file by doing a text search for "migrate".
Remember to test and confirm that all records which were in the old tables can be seen on the patient allergy screens: http://devtest01.openmrs.org/openmrs/coreapps/clinicianfacing/patient.page?patientId=292c2e9a-434a-432d-9e13-1f5ec036bdb6 and http://devtest01.openmrs.org/openmrs/allergyui/allergies.page?patientId=7844&
When all this is done, the old tables should be deleted by a couple of new changesets in "liquibase-update-to-latest.xml".