when marking input items as processed, ensure parse data matchesHEADmaster

After processing the last item for a named machine, mark only those items with
the same ParseData pointer as processed. Previously, we would mark all
preceding items as processed. This is wrong and is a problem for sequences
like:

  machine A // some defs
  machine B // some defs
  machine C // some defs
  machine A // last
  machine B // last
  machine C // last

Once the second A block is seen, then the first A, B and C would all get marked
as processed and ready for writing, even though B and C were not complete yet.

Also, now processing items with no ParseData pointer earlier by immediately
marking them as processed and moving the last flushed pointer forward even if
we didn't process an item with a parse data pointer.

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