Permissions on user level

Do granular permissions on user lever still work, or we can only use Roles to set the permissions now?

I tried to set user permissions to squidex.admin.* and squidex.apps.staging.* but the user has no access to the app untill I add him as a contributor with a role assigned.

Also the role permissions seem to overwrite the user permissions.

Yes, they work and I use them to solve support requests.

But when you assign them the user has to login and to logout again (I know it is annoying).

Yes, that makes sense now
Another thing is, when a user has access only to certain schemas he can no longer see them in content but still has read only access to all schemas. Is it possible to either remove schemas option in UI completely or remove some schemas from there?

No, the permissions are driven by what you need to make the frontend work. Not what you should see.

For example: To make the content list work you need permission to view the schemas, therefore the GET schemas endpoint is always given as a permissions. The same for languages.

But there is a feature request for that: Separate UI and content permissions logic