With version 1.6 of the plugin, the JAXB XJC tool is invoked with the absolute path to the xsd directory as last argument (/repository/a/src/main/xsd). That works as well, since the XJC tool then automatically generates Java code from all schema files in that directory.
After the 2.1 release about a week ago, the build process of one of our multi-module projects started to fail. For some reason, the problem only occurs when run under Linux. On Windows everything works as before.
Basically, we have the following (or similar) directory structure: