refactor: reorganize analysis data to support multiple runs

Strategy: key runs by bicorder version (not date), promote shared inputs
to analysis/data/, and stamp every output with its bicorder_version so
a re-run on edited gradients is self-describing.

Data layout:
- Promote the shared protocol inputs out of the run directory:
    analysis/data/protocols_edited.csv  (411 cleaned protocols)
    analysis/data/protocols_raw.csv     (774 un-cleaned entries)
- Rename the v1.2.6 synthetic run:
    data/synthetic_20251116/ -> data/synthetic_1.2.6/
  so the bicorder version it was scored against is explicit (gradient
  structure changes between versions make date-based names ambiguous)

Provenance:
- bicorder_analyze.py now writes a 'bicorder_version' column into every
  output readings.csv, recording which gradient structure produced it

Scripts:
- Update the real code defaults that pointed at the old run path
  (bicorder_classifier.py, classify_readings.py, sync_readings.sh,
  compare_analyses.py) and refresh docstring/help examples
- Remove a stray committed __pycache__/.pyc

Docs: analysis/README.md documents the new layout + how to add a run;
WORKFLOW.md, TEST_COMMANDS.md, INTEGRATION_GUIDE.md paths updated.

analysis/scripts/visualize_clusters.py

@@ -3,7 +3,7 @@
 Create visualizations of k-means clusters overlaid on dimensionality reduction plots.
 
 Usage:
-  python3 scripts/visualize_clusters.py data/synthetic_20251116.csv
+  python3 scripts/visualize_clusters.py data/synthetic_1.2.6/readings.csv
   python3 scripts/visualize_clusters.py data/manual_20260101.csv --results-dir analysis_results/manual_20260101
 """
 
@@ -20,11 +20,11 @@ def main():
         formatter_class=argparse.RawDescriptionHelpFormatter,
         epilog="""
 Example usage:
-  python3 scripts/visualize_clusters.py data/synthetic_20251116/readings.csv
+  python3 scripts/visualize_clusters.py data/synthetic_1.2.6/readings.csv
   python3 scripts/visualize_clusters.py data/manual_20260101/readings.csv --analysis-dir data/manual_20260101/analysis
         """
     )
-    parser.add_argument('input_csv', help='Diagnostic readings CSV (e.g. data/synthetic_20251116/readings.csv)')
+    parser.add_argument('input_csv', help='Diagnostic readings CSV (e.g. data/synthetic_1.2.6/readings.csv)')
     parser.add_argument('--analysis-dir', default=None,
                         help='Analysis directory (default: <dataset_dir>/analysis)')
     args = parser.parse_args()