Re-upgrading CWL files

When I run cwl-upgrade on a set of CommandLineTools that I have in a directory, I can upgrade them one at a time and test they are okay.

I then have my workflows 1 directory above and upgrade them one at a time. During this process, the individual tools in the tools folder get upgraded/rewritten to the current working directory instead of the directory they were read from. Two things about this:
1. Since the tools were already upgraded, I don't think they need to be rewritten to the current working directory. That pollutes the filesystem.
2. The tools that do need to be upgraded should be rewritten to the directory they were read from.

Is it possible to provide options for both of the above, namely,
1. Only upgrade the cwl provided as input, and not dependent cwl files
2. Write upgraded CWL files to the same directory where they were read from; and instead of overwriting the existing CWL file, give it a new name or output to STDOUT.

Start with the cwl-upgrade command and reproduce the directory workflow described in the issue, upgrading tools before the workflow that references them. Done means the command supports controlling dependent-file upgrades and places any rewritten CWL files according to the requested output behavior, without polluting the current working directory.

Written by the indexing model from the issue text.