JIRA Core is now an application. If you're using JIRA, then you're using JIRA Core.
JIRA Software runs on top of JIRA Core. Same framework, uses a lot of the Core, but the easiest way to think of it is that it "adds lots of functions to JIRA Core"
You *can* have separate users. If you licence 25 people for Core, then they'll be able to use all the standard JIRA functionality. Then you add 25 Software users. Those people can use Scrum and Kanban boards, but also have full access to Core functions (An application licence gives the user Core access automatically)
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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