The vocabulary files that are included there are only those that are available to the public. There are some that must be obtained individually be end users (e.g., because they’ll have to apply for a license or sign some sort of end user agreement or something like that). Details about the value sets that are not available are provided here, highlighted in yellow: https://oncprojectracking.healthit.gov/wiki/display/CRIGTT/Vocabulary+Data+Sets+Source+Documentation
Dan (ONC) (and thanks to Wendy Blumenthal)