How do I know the running version of my bot is the latest one and not the one prior due to e.g. some unfortunate mishap somewhere in the cloud?
If you really worry about it you can use git tags to mark each version and then after uploading download the last bot and unzip it to your local forlder. Git will hightlight any difference in files.
The question really was how do I know Halite servers are running the most recent code. There is no way to identify anything. I know this is highly unlikely but there could also be an unfortunate one-off error resulting in an older code being run.
If you really think the halite game servers have a problem, you can test the servers by making a bot that has some distinctive behavior, and checking for it. For example, all bots move north on turn 100. Then just watch the replays.
Otherwise, if you are just concerned about what the halite contest system has, just download your most recent bot and check that the code is right.