If we purchase a downloaded license for Atlassian products, we are provided the source code, and 12 months of free updates & maintenance.
If we modify the source code in order to customize these products, will we still be able to get product updates?
Are these updates likely to break our products because of our customizations?
You will need to reapply your changes on each upgrade. The upgrade process will tell you which files have been modified. It is definitely a headache if you have a large number of changes. A small number of changes is still just a pain. I have changes to css and to email templates and I do not like applying them, especially when they do not work anymore.
Yes, it will wipe out your modifications - there's no way an upgrade process can know what you've done to any files, and all an upgrade is, is new versions of files, which will overwrite what you've done.
I keep all the modifications in source control, so our upgrades are a doddle - download new war, get changes from source control, rebuild war and install it (obviously, testing each of our changes still work).
As Norman says though, core changes are a last resort - try to do it with config, plugins etc, less fuss on upgrade.
Your data will be carried over fine, as long as you have not changed the core of the database.
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