Revise the JFM research workflow documentation to clarify project structure, decision-making processes, and tool routing. Remove outdated figures and images that are no longer relevant to the current manuscript. Ensure that the workflow aligns with the latest research objectives and safety protocols.
Track the research dossiers, section freezes, supporting manuscript materials, and round-aware agent controls so future drafting decisions can be reviewed across both repository mirrors.
Co-authored-by: Cursor <cursoragent@cursor.com>
Add a canonical src package index, synchronize cross-project status and root navigation, and ignore local generated/runtime payloads while preserving the documented solver and evidence boundaries.
Co-authored-by: Cursor <cursoragent@cursor.com>
Freeze the contract-audited discovery, closed-loop validation, robustness, plotting, and manuscript evidence so the SR section is reproducible and ready for paper development.
Co-authored-by: Cursor <cursoragent@cursor.com>
- Remove obsolete docs (OID_handover, SR_analysis_results, ccd_* handover)
- Remove CCD legacy output_redux and old scripts
- Remove SR old sindy scripts and compare modules
- Update .gitignore to cover all analysis-generated outputs
- Retain all active code in OID/SR/CCD analysis directories
Co-authored-by: Cursor <cursoragent@cursor.com>
Add comprehensive project report (292 lines, 7 figure references)
and handover notes for the next agent.
Co-authored-by: Cursor <cursoragent@cursor.com>
Core changes:
- New phase-state features (PHASE_STATE_KEYS, ILLUSION_PHASE_KEYS) with obs dynamics
- Derivative and absolute output modes (output_mode="deriv"|"absolute")
- predict_v23_deriv() with integration support for closed-loop
- Offline multi-step rollout evaluator (eval_rollout.py)
Key results:
- Illusion 0.75L/1L: phase-state+error-state+abs achieves 0.974/0.958 closed-loop
with zero action history features — proving the new route works
- Karman re100: phase-state+abs reaches 0.699 (vs 0.901 with action history)
- 1.5L confirmed as bang-bang regime (R2=0.12 for linear SINDy)
- Feature ablation: 6-dim phase-state outperforms 16-dim full-lag in closed-loop
Documentation:
- docs/SR_analysis_results.md: comprehensive analysis report
- docs/HANDOVER_SR_ANALYSIS.md: handover notes for next coder
- 6 figures in docs/figures/SR_analysis/
- Updated README.md, sindy_sr_notes.md, sindy_sr_knowledge.md
- Updated configs.py with generalization scenes
Co-authored-by: Cursor <cursoragent@cursor.com>
Frank14f