refactor: improve verification workflow with visual comparison

Major changes:
- paper-image-extractor: Generate reference_plots.py for visual verification
- paper-director: Add image understanding checkpoint with side-by-side comparison
- paper-analyzer: Add data source labeling with reliability levels
- code-writer: Change from TDD to VDD (Verification-Driven Development)
- test-runner: Generate comparison reports with images and explanations
- verification skill: Add difference classification system
- code-generation skill: Emphasize result independence

Key principles:
- Code results are authoritative, paper values are references
- Differences are expected and documented, not bugs to fix
- Visual comparison prioritized over exact numerical match
- Tests verify sanity (shape, gradient, range), not exact values

.opencode/skills/code-generation/SKILL.md

@@ -17,6 +17,36 @@ Guidelines for translating paper descriptions into working PyTorch code.
 2. **Testability**: Write code that can be unit tested
 3. **Readability**: Prefer clarity over cleverness
 4. **Modularity**: One component per file
+5. **Independence**: Code logic based on paper methodology, NOT reverse-engineered from expected outputs
+
+## Critical: Result Independence
+
+The code must implement the **paper's described method**, not be reverse-engineered to match reference values.
+
+### DO NOT:
+```python
+# WRONG: Using values from reference_plots.py as targets
+expected_accuracy = 0.952  # Copied from paper figure
+assert abs(accuracy - expected_accuracy) < 0.01  # This defeats the purpose
+```
+
+### DO:
+```python
+# CORRECT: Implement the method, let results be what they are
+# Paper Section 4.1: "We use Adam with lr=1e-4"
+optimizer = torch.optim.Adam(model.parameters(), lr=1e-4)
+
+# Run training, record actual results
+accuracy = evaluate(model, test_loader)
+# This accuracy is authoritative - compare with paper in report
+```
+
+### Reference Values Are For Comparison Only
+
+Values from `image_understanding.md` and `reference_plots.py` should:
+- Be used in the **final report** for comparison
+- **NOT** be used as assertion targets in tests
+- **NOT** influence implementation decisions
 
 ## Paper-to-Code Mapping
 
@@ -199,3 +229,5 @@ Before completing a module:
 - [ ] Example in docstring works
 - [ ] No hardcoded dimensions (use params)
 - [ ] Gradient flow verified (no in-place ops breaking autograd)
+- [ ] **No reference values hardcoded as expected outputs**
+- [ ] **Implementation based on paper method, not reverse-engineered from results**