The Ship of Harkinian's versioning system is a unique system, comprising of a three-numbered version (x.y.z) and a version codename. The main version number x signifies major feature updates that require a new oot.otr file. The version number y signifies major feature updates and bugfixes that do not require a new oot.otr file. The version number z signifies minor updates such as a collection of bugfixes.
The version codename consists of a sci-fi film character followed by a phonetic alphabet code word. The film character represents a major release version which increments with the major x or y version bumps. The code word represents a minor release version which increments with the minor z version bump.