This commit https://github.com/windup/windup/commit/53c5fe5815 caused all my tests to start failing, because all the test classes are under the org.jboss package, so the test archives are identified as "3rd party" archives.
This is unfortunate (and I'd call that a questionable choice, at least for Windup invocations over single archive), but I can kinda understand it. The problem is that even if I use --packages org.jboss, the archive is ignored.
That's a bug inside the newly-introduced PackageNameMapping.isExclusivelyKnownArchive method – it calls javaConfigurationService.shouldScanFile(classname), which expects/a/file/path, but a.class.name is passed instead.
The fix is simple (use javaConfigurationService.shouldScanPackage instead), so I'm gonna send a PR with that.