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Addresses https://github.com/Kotlin/dokka/issues/534
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Fixes https://github.com/Kotlin/dokka/issues/511
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Package suppression depended on the order of `perPackageOption`s. That should not be the case. Fixes https://github.com/Kotlin/dokka/issues/521
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Fixes https://github.com/Kotlin/dokka/issues/510
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Fixes https://github.com/Kotlin/dokka/issues/514
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