Only (try to) install dependencies when needed in run script

This PR tries to address the fact that `./run.py` might try to install depencies a little too aggressive.

Here the `update_missing_args` method now updates a *"hidden"* flag/argument called `ARGS._install_dependencies`; which controls whether the dependencies are to be installed or not.

It is injected using `PARSER.set_defaults(_install_dependencies=False)` and doesn't show up on the help comments, as it is just a process value (based on the arguments given to the run script).