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How to restrictions all the users from accessing all Jira projects only?

 How to restrictions all the users from accessing all Jira projects only, and user should be able to access the confluence spaces.

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Jira has a permissive model, not a restrictive one.  You can't restrict people from projects, you have to remove what is granting them access.

Pick a project you want to "restrict", and look at the permissions.  You will find something in there saying "Who can see the project:  <rules>".  You'll need to remove whatever rule is letting in your users.

By default, the rules tend to include things like "any logged in user".  That particular rule means anyone who can log in can see the project, so you'll need to remove that permission, and replace it with one that only lets in the people who should see the project.  So something like "group: X" or "project role: Y"

For Confluence spaces, that's a similar principle, but done in Confluence in the space permissions.

Actually, we are planning to migrate Jira cloud site to another existing Jira cloud site. Considering the number of projects that we have, changing permissions project-by-project wont be possible for us to restrict the logged-in users from changing any Jira data. So, just for the migration window, is there any way by which we can indicate the logged-in users that they are accessing the legacy site? e.g. changing the theme color in site, putting one liner note for everyone, etc. 

Annoyingly, Jira Cloud does not have a banner function like Server has had since version 2!

But yes, you can change the colours from Admin -> look and feel.  I find a strong red or black and yellow theme sends the right message.

I also tend to change the site logo to a warning of some sort, and the title text, which will appear in the menu next to the logo!

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