I was right where you are, on Monday. Here is the bat file that I came up with, and just ran it (doesn't matter from where):
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set JDBC_DRIVER=%ORACLE_HOME%\jdbc\lib\classes12.zip
set HIBERNATE_HOME=c:\test\hibernate-2.0.3
set CORELIB=%HIBERNATE_HOME%\lib
set LIB=..\lib
set PROPS=%HIBERNATE_HOME%\src
set CP=%JDBC_DRIVER%;%PROPS%;%HIBERNATE_HOME%\hibernate2.jar;%CORELIB%\commons-logging.jar;%CORELIB%\commons-collections.jar;%CORELIB%\commons-lang.jar;%CORELIB%\cglib.jar;%CORELIB%\dom4j.jar;%CORELIB%\odmg.jar;%CORELIB%\xml-apis.jar;%CORELIB%\xerces.jar;%CORELIB%\xalan.jar;%LIB%\jdom.jar;%LIB%\..\hibernate-tools.jar
java -cp %CP% net.sf.hibernate.tool.hbm2java.CodeGenerator -output=C:\test\java\ C:\test\*.xml
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Also, check this thread out for how to do this as an ant task along with middlegen:
http://forum.hibernate.org/viewtopic.php?t=924447
-Kat