I've been evaluating the cloud based version of JIRA but am thinking we need to go with the server based software. If we have software engineers that will need to greatly modify the current system. I don't think they have that ability with cloud based, right?
I wouldn't recommend "greatly modify" itself, as any code changes will make it unsupported and usually make upgrades a lot harder. I'd strongly recommend implementing customisations as add-ons (barring the two standard hacks Atlassian themselves recommend - changes to emails and release notes)
But, yes, you are right. With Cloud, you can't touch the core products in the slightest, and you can't install most "type 2" plugins (which are the ones you need to use or write if you want to make significant additions or changes to it). If your changes could all be done as "Connect" addons, then you can do them on Cloud, but these really only have access to the REST functions.
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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