Using --cachedir option leaves output of workflow in cache instead of the directory the workflow is run

The title basically sums it up. When running `cwl-runner` and specifying a `--cachedir`, the output that was previously placed in the directory the workflow is run is instead left nested in the cache.

Shouldn't the use of `--cachedir` be transparent to the function of the tool, and leave the "interface" of the tool the same? IE, the output should go to the same place whether you are using `--cachedir` or not.