I have a project with 3 different doxygen documentations. Each of them has it's own warnings-file. For example Projects\Doxygen\warning.txt, Projects\Doxygen\ModuleTestsWarning.txt, Projects\Doxygen\IntegrationTestsWarning.txt.
The Project page has several "Doxygen Warnings" links on the left side but they all link to the same page and the all link to the same page "jenkins/job/Hit1k-1_V01/warnings10" where it says that there are 15 new Warnings, but it is not posible to see in which file. If I click the link with these 15 new warnings i come to page "warnings10Result/new/?" where it says, that there are 0 new warnings. So it seem as if the plugin mixes the information of the three warning-files.