Update command line tool for v5

[nojaf]

For v5 I'd like to remove the --stdin, --stdout and --fsi flags.
I'm not aware of anybody using this and these options are untested in the codebase.

Next, I'd like to change the meaning of the --force flag.
We currently don't change any code if the result isn't valid.
The --force flag should print anyway instead.
This will be useful to detect any bugs from the command line.