Set default arguments in cwltool.factory.Factory

[ThomasHickman]

In the README, the recommended way to use cwltool as a factory is to use the cwltool.factory.Factory class (https://github.com/common-workflow-language/cwltool#import-as-a-module). However, this doesn't set default command line options - these are normally set in the command line using argparse in main by:

cwltool/cwltool/main.py

Line 756 in f691bf1

args = arg_parser().parse_args(argsl)

If no default command line options are passed when instantiating the Factory, then this produces lots of unintended effects (e.g. use_container is False)

[anton-khodak]

Can be merged with #567