Merge branch 'js/empty-index-fixes'

A few places failed to differenciate the case where the index is truly empty (nothing added) and we haven't yet read from the on-disk index file, which have been corrected. * js/empty-index-fixes: commit -a -m: allow the top-level tree to become empty again split-index: accept that a base index can be empty do_read_index(): always mark index as initialized unless erroring out