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app-doc/doxygen: Forward-port qconf workaround for portage-multilib users. Add missing patches and drop some unused ones.

(Portage version: 2.2_rc69-r1/hg/Linux x86_64, signed Manifest commit)
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#see portage manpage
# eclasses provided by java-overlay take precedence over identically named
# eclasses that are provided by gentoo
masters = gentoo
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