It appears that the "auto discovery" feature of the Doxygen plugin forgets to include the projects root folder, utilizing only the job's root workspace, when determining the location of the HTML output folder. I believe this is also related to JENKINS-5424 and JENKINS-6060. This prevents full usage of the Plugin now that the "Use the Doxygen HTML directory" option was removed in version 0.5. The Output Folders can still be published if I use DocLinks Plugin or set the "local module directory" to "." (effectively making the root of the workspace the same as the root of the project files).

Here is the scenario

Source Code Management
---------------------------
Workspace
Repository URL - svn://127.0.0.1/myproject/trunk
Local module directory - trunk
Doxyfile Path Relative to root of workspace - trunk/doc/doxygen.cfg
Doxygen OUTPUT_DIRECTORY - ./doc

When the builds run I end up with an invalid location as seen below
hudson.AbortException: The directory 'E:\hudson\workspace\myproject\./doc\.\doxygen_html' doesn't exist. The url should actually be 'E:\hudson\workspace\myproject\trunk\./doc\.\doxygen_html' instead.

If the Local module directory changes to "." and the Doxfile Path is changed to "doc/doxygen.cfg" then this works without a problem.