first of all, what you're asking of your JIRA might be a lot :)
Anyway, hard numbers on when JIRA stops performing well can not be given, as this is allways a combination of the amount of data (and which dat) and your configuration (e.g. custom fields).
Whalt I could tell you is that the number of Users does not matter at all. Also hundreds of project should not caus a pain, unsure about thousands though (as this could be 2.000 or 900.000...). Billions of issues might seem a bit steep, but I would say it still could work out depending on your configuration. If you want to have some numbers as guidline, I strongly suggest to check out this page in the official documentation. Generaly speking, Atlassian improed JIRA's performance a lot in JIRA 5.1 so this might just be worth a try.
In order ot get more detailed information, you could also try the JIRA data generator, described here.
And just in case JIRA is not 'fast' enough, yuo could just split your future JIRA instance and connect them via application links, so they act (mostly) like it's still one system (from a user's perspective).
Hope that helps? Cheers, David
The number of users does matter in large scale installations - it caches a user list (less of a problem in later versions, but large numbers of users still have an impact when people are searching/selecting on them). More important is the number of concurrent users though - the main Jira performance problems I've seen are things like the "Thursday weekly meeting, so 50 people all need to run filters at the same time" effect.
Jira should not be ruled out if you think Jira is proprietary. You can get access to the source code that Atlassian produces as noted in the FAQ. Atlassian has a special group concentrating on enterprise issues, so you have a good chance that Jira could work for you.
Plugins are another story since many are independently developed, but that does not mean you cannot strike a deal depending on what you need. I would guess you would get a better response if you pay those developers for any special modifications that may be required.
I would expect special governmental issues like multi-level security would need to be commissioned.
As alluded by David's answer, Jira could be federated depending on which groups needs to see each others issues.
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