I have a very similar issue here where I’m using the maven-jaxb2-plugin to generate code from xsd files.
I was able to track down the problem to namespace resolution. Basically the files have to be presented in such way that the order of the files represents the order of dependencies. I would expect the namespace resolver to be able to use the files in parameter as it would a catalog and to iterate the whole collection before failing to resolve a namespace.
As it stands we could summarize the situation as such:
"In order to get XJC to parse and resolve namespaces in the xsd files I must first parse and resolve the xsd files to determine namespace dependencies. Then build the file list accordingly before passing over to xjc"
When viewed like this, I would more consider this a bug than enhancement. This being said, getting this fixed is to me far more important than the categorization semantics.
The maven-jaxb2-plugin seems to use the lexicographical order of files as the order provided to xjc. More details on the issue I raised over there https://github.com/highsource/maven-jaxb2-plugin/issues/98
Should you need more info, details or repro-steps for this issue please let me know.