There are two .jar files in this folder.

CodexDacanium.jar contains the (somewhat) experimental new code of CD: Terra Beta 1.0, with all its new features such as new building levels and the combat overhaul. Choose this one for the full CD: Terra experience.

CodexAlpha136.jar contains the more stable Alpha 1.3.6 code, which is the same as WotEC Alpha 1.3.5 but with Beta 1.0 bug fixes and minor, non-gameplay related changes. Choose this one to continue old saves made in Alpha 1.3.5.