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/INTEGRATION_GUIDE.md

@@ -12,7 +12,7 @@ This guide explains how to integrate the cluster classification system into the
 
 **Version-based compatibility**: The model includes a `bicorder_version` field. The classifier checks that versions match. When bicorder.json structure changes:
 1. Increment the version number in bicorder.json
-2. Retrain the model with `python3 export_model_for_js.py`
+2. Retrain the model with `python3 scripts/export_model_for_js.py data/readings/synthetic_20251116/readings.csv`
 3. The new model will have the updated version
 
 This ensures the web app and model stay in sync without complex backward compatibility.
@@ -20,8 +20,8 @@ This ensures the web app and model stay in sync without complex backward compati
 ## Files
 
 - `bicorder_model.json` - Trained model parameters (5KB, embed in app)
-- `bicorder-classifier.js` - JavaScript implementation
-- `bicorder-classifier.d.ts` - TypeScript type definitions
+- `web/bicorder-classifier.js` - JavaScript implementation
+- `web/bicorder-classifier.d.ts` - TypeScript type definitions
 
 ## Quick Start
 
@@ -38,8 +38,8 @@ cp bicorder_model.json ../path/to/bicorder/public/
 Copy the JavaScript module to your source directory:
 
 ```bash
-cp bicorder-classifier.js ../path/to/bicorder/src/lib/
-cp bicorder-classifier.d.ts ../path/to/bicorder/src/lib/
+cp web/bicorder-classifier.js ../path/to/bicorder/src/lib/
+cp web/bicorder-classifier.d.ts ../path/to/bicorder/src/lib/
 ```
 
 ### 3. Basic Usage
@@ -395,8 +395,8 @@ console.log(classifier.predict(boundary));
 
 ## Questions?
 
-See the demo in `bicorder-classifier.js` for working examples, or test with:
+See the test in `web/test-classifier.mjs` for working examples, or test with:
 
 ```bash
-node bicorder-classifier.js
+node web/test-classifier.mjs
 ```