This is not something I would recommend doing. You'll have to maintain it on all upgrades, and the code might not be as simple as you think. As for where to do it, I would start with a *test* system. You'll need to find the right files (I've done similar things in old versions of JIRA, but the files have changed since I last did it, so I can't help you), change them, keeping *very* careful notes on what you've done, and then restart JIRA to pick up the changes. Once happy in your test system, backup your production install and apply the changes.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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