There are several team in our company, we granted permission to browse project (view issues inside those projects) only to authorized groups. This works fine, but is there a way to hide those projects completly? So they won't be shown in "View All Projects"
They should be completely invisible to people who do not have "browse" permissions for the projects.
(As an administrator, you get to bypass this partly - you can always get the full list of projects you can administrate, even if you don't have browse for them)
Ah, yes, that is a bit of a quirk. It does make sense when it's explained and thought through, but it's really NOT intuitive. You'll have the same problem with reporter. It's a lot more complex than this, but the way I try to simplify it is that Jira is thinking of people who could be the reporter/assignee, rather than who currently is.
You can enable a couple of options that make it behave more intuitively, but I'm not sure it's that helpful for you yet. (They're turned off by default because they can cause problems in the hands of inexperienced administrators).
If you're interested, it's covered at https://confluence.atlassian.com/display/JIRA/Current+Reporter+Browse+Project+Permission
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