That's right, doxygen.html would need an update.
Altough the plantuml support in the 1.8.8 release of doxygen is great news, it suffers from the lack of some advanced features, to name a few:
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@pauseuml, @unpauseuml, @appenduml are missing
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@startuml{filename, caption, size_options_etc} not taking extra arguments
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no ability to configure:
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path to java application launcher
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any options before -jar (eg. include path)
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any options after -jar, for plantuml (eg. defines, ..)