Config Replacement in Snakemake

This work was completed as part of the Snakemake Hackathon 2025. Previously, when a configuration file was specified via the Snakemake CLI (e.g., `snakemake --config config.yaml`), the contents of that file were *merged* with any configuration variables already defined within the Snakefile. This meant that the CLI config would only extend or update existing values, rather than completely replacing the workflow's default configuration. This work item introduces the `--replace-workflow-config` parameter to the Snakemake CLI.