This is your mistake. That command wipes out the Vagrantfile that we provide. Our README makes no mention of running this command. You'll need to run vagrant destroy to destroy the VM you've created and then run git checkout -- Vagrantfile to restore the copy we provide before running vagrant up.
As Evan mentioned, don’t run vagrant init as this will wipe out the Vagrantfile that App Inventor provides. Any reason for you to use this command in the first place? There isn’t any mention of it in the README. Hope this answered your question.
Follow the instructions in this section of the readme and it should work. As @bartmathijssen already mentioned, do not run vagrant init because it wipes out our actual initialization file with a blank version.