We have incorrect "Effective Permission" indicator on category permissions tab. For example I have "CATEGORY.ADD" permission set for category with ID = 0 (doesn't exist in database). When I view "Content" category permissions, which is child category of that category, then I see, that "CATEGORY.ADD" permission is inherited from it's parent (Home), but it shows, that it's denied (red circle), but it's actually allowed (green).
I think, that problem is related to case, that that top category doesn't exist in database. If there will be difficulties to fix that indicator, then at least we can transfer permissions from 0 category to Content category to fix indicator this way.
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