I used the following command to generate JAXB stubs from mzXML.xsd:

G:\tmp\_grabage\mzxml>
    "C:\Program Files\Java\jdk1.7.0_75\bin\xjc.exe"
    -b bindings3.xml
    -d generated
    -p umich.ms.fileio.filetypes.mzxml.jaxb
    http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_3.2.xsd

There was a problem caused by "general_types_1.0.xsd", which used the same attribute name twice ("value").
This was resolved by providing "-b bindings3.xml" option to xjc, this was the file providing mappings to new names.

