The easiest way to figure this out is to look in the imsmanifest.xml file at the root of the course. Near the tip of the course, there might be a metadata tag (it will be required in 2004). If the schemaversion element in the metadata tag says "CAM 1.3" or "SCORM 2004 3rd Edition", then it is a SCORM 2004 course. Otherwise it is 1.2.
How do I differentiate between a SCORM 1.2 and a SCORM 2004 course?
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You can also look for the default XML namespace. This is contained in the xmlns attribute of the root node of the manifest. If it's " http://www.imsglobal.org/xsd/imscp_v1p1", the file is SCORM 2004.