Reorganize directory, add manual dataset and sync tooling

- Move all scripts to scripts/, web assets to web/, analysis results
  into self-contained data/readings/<type>_<YYYYMMDD>/ directories
- Add data/readings/manual_20260320/ with 32 JSON readings from
  git.medlab.host/ntnsndr/protocol-bicorder-data
- Add scripts/json_to_csv.py to convert bicorder JSON files to CSV
- Add scripts/sync_readings.sh for one-command sync + re-analysis of
  any dataset backed by a .sync_source config file
- Add scripts/classify_readings.py to apply the LDA classifier to all
  readings and save per-reading cluster assignments
- Add --min-coverage flag to multivariate_analysis.py for sparse/shortform
  datasets; also applies in lda_visualization.py
- Fix lda_visualization.py NaN handling and 0-d array annotation bug
- Update README.md and WORKFLOW.md to document datasets, sync workflow,
  shortform handling, and new scripts

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

analysis/TEST_COMMANDS.md

@@ -7,7 +7,7 @@ Run these tests in order to verify the refactored code works correctly.
 Test that prompts are generated correctly with protocol context:
 
 ```bash
-python3 bicorder_query.py protocols_edited.csv 1 --dry-run | head -80
+python3 scripts/bicorder_query.py data/readings/synthetic_20251116/protocols_edited.csv 1 --dry-run | head -80
 ```
 
 **Expected result:**
@@ -21,7 +21,7 @@ python3 bicorder_query.py protocols_edited.csv 1 --dry-run | head -80
 Check that the analyze script still creates proper CSV structure:
 
 ```bash
-python3 bicorder_analyze.py protocols_edited.csv -o test_output.csv
+python3 scripts/bicorder_analyze.py data/readings/synthetic_20251116/protocols_edited.csv -o test_output.csv
 head -1 test_output.csv | tr ',' '\n' | grep -E "(explicit|precise|elite)" | head -5
 ```
 
@@ -36,7 +36,7 @@ head -1 test_output.csv | tr ',' '\n' | grep -E "(explicit|precise|elite)" | hea
 Query just one protocol to test the full pipeline:
 
 ```bash
-python3 bicorder_query.py test_output.csv 1 -m gpt-4o-mini
+python3 scripts/bicorder_query.py test_output.csv 1 -m gpt-4o-mini
 ```
 
 **Expected result:**
@@ -61,7 +61,7 @@ Verify that the tool doesn't create any conversation files:
 llm logs list | grep -i bicorder
 
 # Run a query
-python3 bicorder_query.py test_output.csv 2 -m gpt-4o-mini
+python3 scripts/bicorder_query.py test_output.csv 2 -m gpt-4o-mini
 
 # After running test
 llm logs list | grep -i bicorder
@@ -76,7 +76,7 @@ llm logs list | grep -i bicorder
 Test batch processing on rows 1-3:
 
 ```bash
-python3 bicorder_batch.py protocols_edited.csv -o test_batch_output.csv --start 1 --end 3 -m gpt-4o-mini
+python3 scripts/bicorder_batch.py data/readings/synthetic_20251116/protocols_edited.csv -o test_batch_output.csv --start 1 --end 3 -m gpt-4o-mini
 ```
 
 **Expected result:**
@@ -106,7 +106,7 @@ with open('test_batch_output.csv') as f:
 Test that model parameter works in dry run:
 
 ```bash
-python3 bicorder_query.py protocols_edited.csv 5 --dry-run -m mistral | head -50
+python3 scripts/bicorder_query.py data/readings/synthetic_20251116/protocols_edited.csv 5 --dry-run -m mistral | head -50
 ```
 
 **Expected result:**
@@ -117,7 +117,7 @@ python3 bicorder_query.py protocols_edited.csv 5 --dry-run -m mistral | head -50
 Test with invalid row number:
 
 ```bash
-python3 bicorder_query.py test_output.csv 999
+python3 scripts/bicorder_query.py test_output.csv 999
 ```
 
 **Expected result:**
@@ -129,11 +129,11 @@ Compare the new standalone prompts vs old system prompt approach:
 
 ```bash
 # New approach - protocol context in each prompt
-python3 bicorder_query.py protocols_edited.csv 1 --dry-run | grep -A 5 "Analyze this protocol"
+python3 scripts/bicorder_query.py data/readings/synthetic_20251116/protocols_edited.csv 1 --dry-run | grep -A 5 "Analyze this protocol"
 
 # Old approach would have had protocol in system prompt only (no longer used)
 # Verify that protocol context appears in EVERY gradient prompt
-python3 bicorder_query.py protocols_edited.csv 1 --dry-run | grep -c "Analyze this protocol"
+python3 scripts/bicorder_query.py data/readings/synthetic_20251116/protocols_edited.csv 1 --dry-run | grep -c "Analyze this protocol"
 ```
 
 **Expected result:**