CLONE - Remove any re-index from the JIRA 4.1 upgrade tasks that's not needed

This is a clone of JRA-18493 which was resolved as fixed.

During an upgrade from Jira 3.13 to Jira 4.1.2 two re-indexes occur, one for Build 440 and one for Build 518.
Please reduce this to one if at all possible.

On a system with many issues, like 200000, this double re-indexing consumes 2 hours of site down time instead of 1 hour.
In our upgrade from Jira 3.13 to 4.1.2, we need to manually re-index a third time as we have dropped and then re-added a custom calculated field that changed due to changes in the Jira API.