i have created a one-in-all ant target, which executes findbugs, checkstyle & pmd for the given $srcDir, $classesDir.
Works as expected, and the Hudson Plugins do their job.

Unfortunately, i just wanted to analyze a specific directory, so i set my $srcDir to $srcDir/com/mycompany/myapp/beans.
($classesDir respectively to $classesDir/com/mycompany/myapp/beans)
Ant targets run as expected, analyzing only this folder, XML output looks fine
Checkstyle & PMD Plugins work as expected, can click till the java sources
Only the findbugs plugin complains about not finding the source file for displaying....

Copying the source file 'com/mycompany/myapp/beans/pitches/PitchDataBean.java' from the workspace to the build folder '/export/home/tomcat/.hudson/jobs/myapp_trunk/builds/2010-08-11_15-14-43/workspace-files/fda28c.tmp' on the Hudson master failed.
Seems that the path is relative, however an absolute path is required when copying the sources.
Is the file 'PitchDataBean.java' contained more than once in your workspace?
Is the file 'com/mycompany/myapp/beans/pitches/PitchDataBean.java' a valid filename?
If you are building on a slave: please check if the file is accessible under '$HUDSON_HOME/[job-name]/com/mycompany/myapp/beans/pitches/PitchDataBean.java'
If you are building on the master: please check if the file is accessible under '$HUDSON_HOME/[job-name]/workspace/com/mycompany/myapp/beans/pitches/PitchDataBean.java'
hudson.util.IOException2: remote file operation failed: com/mycompany/myapp/beans/pitches/PitchDataBean.java at hudson.remoting.LocalChannel@15bbe8
at hudson.FilePath.act(FilePath.java:749)
at hudson.FilePath.act(FilePath.java:735)
at hudson.FilePath.copyTo(FilePath.java:1360)
at hudson.plugins.analysis.core.HealthAwarePublisher.copyFilesWithAnnotationsToBuildFolder(HealthAwarePublisher.java:264)
at hudson.plugins.analysis.core.HealthAwarePublisher.perform(HealthAwarePublisher.java:226)
at hudson.tasks.BuildStepMonitor$2.perform(BuildStepMonitor.java:27)
at hudson.model.AbstractBuild$AbstractRunner.perform(AbstractBuild.java:601)
at hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:580)
at hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:558)
at hudson.model.Build$RunnerImpl.post2(Build.java:158)
at hudson.model.AbstractBuild$AbstractRunner.post(AbstractBuild.java:528)
at hudson.model.Run.run(Run.java:1280)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46)
at hudson.model.ResourceController.execute(ResourceController.java:88)
at hudson.model.Executor.run(Executor.java:127)
Caused by: java.io.FileNotFoundException: com/mycompany/myapp/beans/pitches/PitchDataBean.java (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:106)
at hudson.FilePath$30.invoke(FilePath.java:1364)
at hudson.FilePath$30.invoke(FilePath.java:1360)
at hudson.FilePath$FileCallableWrapper.call(FilePath.java:1899)
at hudson.remoting.LocalChannel.call(LocalChannel.java:45)
at hudson.FilePath.act(FilePath.java:742)
... 14 more