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/classify_readings.py

@@ -9,7 +9,7 @@ classified — though with lower confidence.
 Usage:
   python3 scripts/classify_readings.py data/manual_20260320/readings.csv
   python3 scripts/classify_readings.py data/manual_20260320/readings.csv \\
-      --training data/synthetic_20251116/readings.csv \\
+      --training data/synthetic_1.2.6/readings.csv \\
       --output data/manual_20260320/analysis/classifications.csv
 """
 
@@ -29,8 +29,8 @@ def main():
     parser.add_argument('input_csv', help='Readings CSV to classify')
     parser.add_argument(
         '--training',
-        default='data/synthetic_20251116/readings.csv',
-        help='Training CSV for classifier (default: synthetic_20251116)'
+        default='data/synthetic_1.2.6/readings.csv',
+        help='Training CSV for classifier (default: synthetic_1.2.6)'
     )
     parser.add_argument(
         '--output', default=None,