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/sync_readings.sh

@@ -7,7 +7,7 @@
 #   scripts/sync_readings.sh data/manual_20260320
 #   scripts/sync_readings.sh data/manual_20260320 --no-analysis
 #   scripts/sync_readings.sh data/manual_20260320 --min-coverage 0.8
-#   scripts/sync_readings.sh data/manual_20260320 --training data/synthetic_20251116/readings.csv
+#   scripts/sync_readings.sh data/manual_20260320 --training data/synthetic_1.2.6/readings.csv
 #
 # .sync_source format:
 #   REMOTE_URL=https://git.example.org/user/repo
@@ -18,7 +18,7 @@ set -euo pipefail
 DATASET_DIR="${1:?Usage: $0 <dataset_dir> [--no-analysis] [--min-coverage N]}"
 RUN_ANALYSIS=true
 MIN_COVERAGE=0.8
-TRAINING_CSV="data/synthetic_20251116/readings.csv"
+TRAINING_CSV="data/synthetic_1.2.6/readings.csv"
 
 shift || true
 while [[ $# -gt 0 ]]; do