JIRA 6.1 permission issues when installing as Root

Steps to Replicate

1. Download JIRA 6.1 Linux installer
2. Run it with Root user
3. Finish the Installation.

Expected Behavior

JIRA's folders would have the correct permissions for user 'jira' and all files would be created without any issues.

Actual Behavior

Jira's folders that are owned by the "jira" user don't have the write permission.
Upon JIRA start, the following error appears in catalina.out:

SEVERE: Unable to create directory for deployment: /opt/atlassian/jira/conf/Catalina/localhost

And the directory above fails to be created.
Note: If the installer is ran by another user, all JIRA folders will have their permissions attached to only the user who ran the command, therefore the issue does not reproduce.

Workaround:

In order to fix this, you can either set the permission of the folder to 777, granting permission to all users, change the owner to root or give the folders the correct permission according to the jira user.

Also, you can use the version 6.2 instead, since this was fixed by then.