CLI options parsing is order-dependent

The parsing of the CLI options is dependent on an arbitrary ordering where associative arguments (flags like `--json`) need to come first before positional arguments. If these associative arguments are provided after a positional argument, they are currently being silently ignored.

Start by locating the CLI options parsing entry point and reproduce the issue with a positional argument before and after --json. Done means associative options are recognized and preserved regardless of whether they appear before or after positional arguments, with coverage for both orderings.

Written by the indexing model from the issue text.