Before I
answer anything else, have you noticed the comments to that
order in README.txt (and in the announcement)?
only in part.. it's a bit sparse on that matter and I must have overlooked
the warning in there.
I will, of course accept contributions to the documentation, as well
as the code.
Though to be honest the fact that file2jack does not move the
transport is in the first paragraph of README.txt (and the webpage) :)
-- Dan