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/WORKFLOW.md

@@ -68,7 +68,7 @@ python3 scripts/json_to_csv.py data/manual_20260320/json/ \
 ### Process All Protocols with One Command
 
 ```bash
-python3 scripts/bicorder_batch.py data/synthetic_20251116/protocols_edited.csv -o analysis_output.csv
+python3 scripts/bicorder_batch.py data/protocols_edited.csv -o analysis_output.csv
 ```
 
 This will:
@@ -81,13 +81,13 @@ This will:
 
 ```bash
 # Process only rows 1-5 (useful for testing)
-python3 scripts/bicorder_batch.py data/synthetic_20251116/protocols_edited.csv -o analysis_output.csv --start 1 --end 5
+python3 scripts/bicorder_batch.py data/protocols_edited.csv -o analysis_output.csv --start 1 --end 5
 
 # Use specific LLM model
-python3 scripts/bicorder_batch.py data/synthetic_20251116/protocols_edited.csv -o analysis_output.csv -m mistral
+python3 scripts/bicorder_batch.py data/protocols_edited.csv -o analysis_output.csv -m mistral
 
 # Add analyst metadata
-python3 scripts/bicorder_batch.py data/synthetic_20251116/protocols_edited.csv -o analysis_output.csv \
+python3 scripts/bicorder_batch.py data/protocols_edited.csv -o analysis_output.csv \
   -a "Your Name" -s "Your analytical standpoint"
 ```
 
@@ -100,12 +100,12 @@ python3 scripts/bicorder_batch.py data/synthetic_20251116/protocols_edited.csv -
 Create a CSV with empty gradient columns:
 
 ```bash
-python3 scripts/bicorder_analyze.py data/synthetic_20251116/protocols_edited.csv -o analysis_output.csv
+python3 scripts/bicorder_analyze.py data/protocols_edited.csv -o analysis_output.csv
 ```
 
 Optional: Add analyst metadata:
 ```bash
-python3 scripts/bicorder_analyze.py data/synthetic_20251116/protocols_edited.csv -o analysis_output.csv \
+python3 scripts/bicorder_analyze.py data/protocols_edited.csv -o analysis_output.csv \
   -a "Your Name" -s "Your analytical standpoint"
 ```