1. Keep track of which options have been used.
2. No longer run the pipeline show options multiple times
   for pipetask qgraph.
3. No longer warn about options not being used when they
   are about to be used.
4. If --show is used, no longer continue on unless there are
   remaining --show options to process.

The latter means that using `pipetask qgraph` with only pipeline
show options exits without building the graph, and any use of
--show leads to `pipetask run` not running anything.

This matches what the click option callback is doing itself
and so ensures consitency in option handling.

Also added some additions.

This is easier to test and it is odd having a class be able to exit.

This makes it easier to test the output.

There is a non-zero chance that people might want to specify
a command-line config option that includes a comma and it's
safer to require people to use multiple --config options.

This makes it clear why the command finished without doing anything.