Upgrading Jira 8 between minor versions will always indicate that setenv.sh has customizations that are not applied

Issue Summary

When upgrading Jira 8 between minor versions (8.6 > 8.8 for example, or 8.10 > 8.11 as another upgrade example), after the upgrade is complete, the admin will see a warning page that explains that some configuration/settings files that contained customizations could not be copied over. This is expected for any startup/installation file where the admin might have made changes. However in this case, the $JIRAINSTALL/bin/setenv.sh file will always appear on this list, even when the admin has made no changes at all to that file.

Steps to Reproduce

1. install Jira Software/Core 8.10.0 (other 8 versions likely affected)
2. Complete the setup and make sure Jira works
3. Make no changes to setenv.sh
4. upgrade that existing installation directory to a newer version, such as 8.11.0
5. start Jira after upgrade

Expected Results

Expecting that there are no actual changes to that setenv.sh file and the initial startup would not indicate there are when you first start Jira after the upgrade.

Actual Results

Admins will always see that the setenv.sh file as having had customized changes to it that have not been applied to the upgraded install

The listed configuration files contain custom changes. To keep your current configuration, re-apply these custom changes to the new version of the files during upgrade.

bin/setenv.sh 

Workaround

• The warning page does not prevent upgrades to Jira in this case. This is just a warning message that appears to be a false positive in most cases. You can still dismiss this and complete the upgrade.
• You can use -Djira.startup.warnings.disable=true startup flag, (see Setting properties and options on startup) which disables Johnson warnings page entirely:

  Disables the page (johnson) that displays errors after starting Jira if there are only dismissible warnings. The page will appear if there are any important errors.