The mods, not sure what's up there.
The game had a long prologue, and the updates were called .01-.07, then changed to C1.E1 when the first official chapter was released. The message was mostly for people who had been playing the prologue chapters to let them know the whole game was still in the one file, and that you could download the current version of the game and still start from scratch.
At this point, it probably is a bit outdated to have the message there, at least for new players who started after episode 1, but it's still valid for anyone who was here for the early prologues and took a break, so it's reasonable to keep it up for that reason.
EDIT: It's also somewhat effective for people who were part of the "Emma's Solo Ending" chapter (which is also not a separate game, but part of the full game and integrated into the whole thing).
Basically, there's only one game file necessary, and it's whatever the current game file is.