I haven't been able to find an option to restrict browsing projects to logged in users only. The only method seems to be to select a group, but I don't currently have a group containing all users.
You've answered your own question almost. You need to restrict browsing to a group or groups that contain the users you want to let in.
Normally, there is a group containing all the users who can log in - jira-users, but I assume you've pulled that from the global permissions.
The short answer is that you probably want to create a group that everyone is in, and use that in the permissions
Sounds like you have to change the modus into "private" on System->General Configuration
Private mode just refers to sign up of users I believe. My instance is set to private already but logged out users can still see issues.
I don't seem to have any group that contains all the Jira users. We sync with active directory, and I don't want to have to manually add users to a group. Unfortunately the AD setup doesn't have a single group that everyone is a member of. Confluence (or maybe Fisheye, I forget which) has an option in its permissions to allow any logged in user, just thought Jira would have the same.
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