--keep-directories and --checksum do not work together

[imerr]

I have been trying to upload a number of files with --keep-directories and due to ia crashing (#597) I have to restart uploads from time to time.
For a previous upload (not using --keep-directories) it would skip files that were already uploaded, but this doesn't seem to work with --keep-directories

I haven't done any digging as to why this might be so far