Looking at: http://gittup.org/tup/ex_dependencies.html

I see the following warning about half way down the page. While I understand the first time this happens tup has an issue, I don't understand why it can't automatically remember it for future use (or does it?)

    *** tup errors ***
    tup error: Missing input dependency - a file was read from, and was not
    specified as an input link for the command. This is an issue because the file
    was created from another command, and without the input link the commands may
    execute out of order. You should add this file as an input, since it is
    possible this could randomly break in the future.