The second patch restores the correct behaviour for popup windows as well. Same-site links are opened in the same popup, everything else is opened in the user's browser. Same-site links with a target other then `_self` are opened in a new tab in the most recent normal Thunderbird window, which is what Firefox is doing in this case as well.
Bug 1585381 Comment 27 Edit History
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The second patch restores the correct behaviour for popup windows as well. Same-site links are opened in the same popup, everything else is opened in the user's browser. Same-site links with a target other than `_self` are opened in a new tab in the most recent normal Thunderbird window, which is what Firefox is doing in this case as well.