Fix --reference filtering + document --fixed-y and --reference usage

[Copilot]

The --reference flag in run_pipeline_driver.py was reading args.reference / args.type directly, bypassing resolve_args() entirely — so any reference_file / assay_types values set in a config JSON were silently ignored. Additionally, --fixed-y (added in #137) was never added to the README, and no usage example existed for --reference.

Code fix

• run_pipeline_driver.py: switch reference filtering to use resolved["reference_file"] and resolved["assay_types"] so the config → CLI priority chain is respected

# Before
if args.reference:
    df = pd.read_excel(args.reference)
    filtered = df[df['Assay'].str.lower().isin([t.lower() for t in args.type])]

# After
if resolved["reference_file"]:
    df = pd.read_excel(resolved["reference_file"])
    filtered = df[df['Assay'].str.lower().isin([t.lower() for t in resolved["assay_types"]])]

Docs (IPNAnalysis/README.md, README.md)

• Add --fixed-y row to the run_pipeline_driver.py CLI reference table
• Add §9: --reference / --type workflow example (with note on required Excel columns)
• Add §10: two-step --fixed-y workflow example
• Add --reference quick-start snippet to top-level README.md

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