No, you can't do that, unforunately. However, you can load multiple configuration files. My solution to exactly this problem was to configure hibernate with mulitple configuration files: one for the application properties (JDBC connections, show_sql="true", etc.), then one for each jar that uses hibernate and the app needs.
Here's a little sample code. sPath is the application's normal .cfg.xml file. mapFiles is a List of names of config files with <mapping> tags, though any confg file is allowed. I get that list from an XML file that configures my app.. you can make it any way you like.
Code:
org.hibernate.cfg.Configuration hibConfig =
new org.hibernate.cfg.Configuration().configure(sPath);
for (String mapFile : mapFiles)
{
hibConfig.configure(mapFile);
}
m_FactSession = hibConfig.buildSessionFactory();