Improve documentation for extract_jump & jump
Make running external commands cleaner.

External commands are now called through an internal command. Among other
things this means you don't need to register commands so it will always
call the latest version. It also means you don't need to deregister it to
stop it from polluting the workspace.
Add print_pipline

This command allows you to see the current state of the pipeline without
having to edit the code that runs the pipeline. Useful for debugging.