I am trying to alter Jira in the same way you can alter Confluence using the custom HTML option in configuration.
Is there an add on or has anyone performed this before?
Our goal is to have a toolbar a the top of every page that provides users with the same look and feel of our organizations website no matter what application is running.
Any help is greatly appreciated.
You could edit the banner and insert HTML, providing the JIRA system admin allows them.
I have stored complex HTML/JS there. You could also explore front end modifications with ScriptRunner's Script Fragments, if you have that add-on.
https://scriptrunner.adaptavist.com/latest/jira/CustomisingUI.html
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