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customisation and customisation_backup folder of Jira

If I do further modification of files Jira is not considering to store them in the according folder 'customisation' or 'cusotmisation_backup' can I just add them? Or will the content be overwritten when I upgrade? When does Jira update what folder according to customisations?

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An upgrade will overwrite all changed files.  You may not be able to just put them back, you'll need to do a diff between each one to see if the format has changed and your customisation is still valid.

New files that you have added will not be touched.

Not all changed files will be overwritten as you say. See here: https://confluence.atlassian.com/support/pre-upgrade-planning-tool-973479832.html
So what about a cacerts file for example? It is stored under <jira-install>/jre/lib/security. This is not going to be considered. And I do have other modified files in locations where it should be considered, but they are neither in customisations folder nor customisations_backup. So it seems the detection for modifications cannot be trusted...

The diff is clear. But I will do it once on a test server to see what changed, then I can prepare the files on all other servers and just go ahead and perform unattended upgrades. So do I need to make the updates in the customisations folder or the customisations_backup folder or both?

Neither - the customisations you are doing are done in-place, as part of the system, not in a separate and unrelated directory.

But how it comes, that I need to replace all the files myself after the upgrade? And overwrite those files coming from the 're-install' of Jira? The setenv.sh is missing parameter settings, etc. So it looks to me like a pretty manual task to be done here or does it just not work via unattended upgrade?

Because the upgrade can't possibly know what you have customised, barring a couple of things, it doesn't attempt to merge your customisations into the known-good files it is creating/updating.

After re-reading your comments, it seems I misunderstood your point. So you're basically saying the upgrade will overwrite any files in the install folder, but modifications of files won't be recovered.
So I don't get the purpose of this two directories then, as even they do not reflect what really was customized. We modified for example the setenv.sh file to include additional parameters, but this file can't be found in the customizations directories. But from the Atlassian Docu this file should be checked and added there. Am I right?

So this means, I would need to store my customisations at those customisation directories as well in order to make an easy comparison and adaption. Otherwise I need to make a diff of the entire install folder...

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