Jira Agile seems closely tied to the Agile approach to software development. Here at our company we have not adopted this scrum, sprint approach to our development cycle and using a tool like that which seems to have many assumptions tied to Agile would just make muddy up our PM effort.
Is there another tool/add-on that could be used in its place with Jira/Confluence?
You could start by simply ignoring Agile in Jira. You don't have to enable it for every project, so you could pull out the non-Agile ones quite easily. Then just work inside Jira as it was built before Agile was added.
It's worth a try - depends on what sort of "non Agile" you're going to try. Jira's workflow and field stuff is quite powerful and most of it isn't hooked into the Agile stuff. Even the "fix version" which does a lot in Agile still has quite a lot of functionality without the Agile plugin.
So I'd give it a shot and see how it fits your processes (and remember, you can change the workflows to match your processes!)
There are also Gantt chart plugins for Jira if you are using traditional project planning (waterfall style, or critical path style).
If you are not Agile Scrum but want to be Agile (Lean), the Kanban mode of Jira Agile could be worthwhile investigating for you. Kanban does not have a notion of sprints but gives you a graphical way of working with tasks and the Jira workflows. We have teams here that are not Agile (yet) and they use Kanban as a stepping stone towards becoming Agile Scrum teams.
I agree with Nic Brough though that plain Jira has some really powerfull workflow and field and screen (dialogs) features. There are however free alternatives if you want to try that first to see if it fits the purpose. RedMine is a notable free tool for this although there are lots of alternatives (zendesk, bugzilla, ceph, ...)
I should say that the company I work for chose not to go with the free alternatives for support reasons. Atlassian has a very responsive support function that is worthwhile the money when you have more than 100 users :-)
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