The major number in Milton's version corresponds to the maximum MLT file format it can read. For instance, Milton x.N.x can read MLT files vN, vN-1, ..., v1. At the time of this writing there is only Milton v1.x.x and MLT v1.
The files src/persist.(c|h), functions milton_save and milton_load serve as
documentation for the file format. If this is not enough, please contact me at
bigmonachus@gmail.com