Doxygen correctly runs in my workspace at
C:\neilt\projects\hudson\jobs\CCode\workspace\top_level\doc\auto_doc
This folder contains the Doxyfile (attached)
The resulting files are correctly placed in
C:\neilt\projects\hudson\jobs\CCode\workspace\top_level\doc\auto_doc\html

My job is configured to publish the doxygen
In the job config page the Doxyfile path is set to
top_level/doc/auto_doc/Doxyfile

I get this at the console :

TASKS] Scanning workspace files for tasks...
[TASKS] Found 292 annotations (0 new, 22 high, 270 normal, 0 low)
[TASKS] Not changing build status, since no threshold has been exceeded
[WARNINGS] Parsing warnings in console log...
[WARNINGS] Found 40 annotations (0 new, 0 high, 40 normal, 0 low)
[WARNINGS] Not changing build status, since no threshold has been exceeded
Recording test results
[DocLinks] Copying FileLocks in c/h files to 1 ...
Sending e-mails to: xxxxxxx
Publishing Doxygen HTML results.
FATAL: error
hudson.AbortException: The directory 'C:\neilt\projects\hudson\jobs\CCode\workspace\html' doesn't exist.
at hudson.plugins.doxygen.DoxygenDirectoryParser.retrieveDoxygenDirectoryFromDoxyfile(DoxygenDirectoryParser.java:292)
at hudson.plugins.doxygen.DoxygenDirectoryParser.invoke(DoxygenDirectoryParser.java:56)
at hudson.plugins.doxygen.DoxygenDirectoryParser.invoke(DoxygenDirectoryParser.java:24)
at hudson.FilePath.act(FilePath.java:694)
at hudson.FilePath.act(FilePath.java:676)
at hudson.plugins.doxygen.DoxygenArchiver.perform(DoxygenArchiver.java:159)
at hudson.tasks.BuildStepMonitor$2.perform(BuildStepMonitor.java:27)
at hudson.model.AbstractBuild$AbstractRunner.perform(AbstractBuild.java:582)
at hudson.model.AbstractBuild$AbstractRunner.performAllBuildStep(AbstractBuild.java:563)
at hudson.model.AbstractBuild$AbstractRunner.performAllBuildStep(AbstractBuild.java:550)
at hudson.model.Build$RunnerImpl.cleanUp(Build.java:158)
at hudson.model.Run.run(Run.java:1240)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46)
at hudson.model.ResourceController.execute(ResourceController.java:88)
at hudson.model.Executor.run(Executor.java:122)
Finished: FAILURE

This seems to imply that Doxygen must be run from the root of the workspace
or
the output path in the doxyfile must be absolute (which is not possible for me)