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I use JAXB with SAXParserFactory to read in a xml that contains other inclusions. For example, this following xml is called “TheFile.xml” and it refers to “class_common.xml” . <!DOCTYPE page [ <!ENTITY class_common SYSTEM "class_common.xml" >]> <api xmlns:denp="http://intranet.denali.com/wiki/DocBook_profiling"> &class_common; But what I notice is the default location used in SAXParserFactory for “class_common.xml” is where I launch the program . For example, my program is stared from DIR1 and both xml files are in DIR2, SAXParserFactory reads the “TheFile.xml” an