JIRA works on the 'grant access' model. Many early JIRA users grant the jira-user group access to projects, which allows everyone access. The first thing is to remove that access. I suggest using the project roles to allow access. That way the individual project admins can add people to the project. If you use groups the JIRA admin will have to move users into the groups. It will take some work to convert, but be much easier to administer in the long run. You'll also be able to limit transitions to particular roles.
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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