Snakemake Usage

V1 has no Snakemake runtime dependency. Call reprotrail run from Snakemake rules as a normal wrapper command.

shell:
    "reprotrail run "
    "--log {log} "
    "--provenance-json {output.prov} "
    "--product-output {output.data} "
    "-- python -m my_project.step --output {output.data}"

Keep project-specific rule expansion, resources, and input selection in the workflow. Keep generic provenance, Pixi environment capture, dependency epochs, and reproduction behavior in reprotrail.