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feat: Add dashboard chat integration and MCP server

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Major changes:
- Dashboard: WebSocket-based chat with session management
- Dashboard: New chat components (ChatPane, ChatInput, ModeToggle)
- Dashboard: Enhanced UI with parallel coordinates chart
- MCP Server: New atomizer-tools server for Claude integration
- Extractors: Enhanced Zernike OPD extractor
- Reports: Improved report generator

New studies (configs and scripts only):
- M1 Mirror: Cost reduction campaign studies
- Simple Beam, Simple Bracket, UAV Arm studies

Note: Large iteration data (2_iterations/, best_design_archive/)
excluded via .gitignore - kept on local Gitea only.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
Anto01
2026-01-13 15:53:55 -05:00
parent 69c0d76b50
commit 73a7b9d9f1
1680 changed files with 144922 additions and 723 deletions
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24
docs/protocols/operations/OP_01_CREATE_STUDY.md
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@@ -3,9 +3,9 @@
<!--
PROTOCOL: Create Optimization Study
LAYER: Operations
VERSION: 1.0
VERSION: 1.2
STATUS: Active
LAST_UPDATED: 2025-12-05
LAST_UPDATED: 2026-01-13
PRIVILEGE: user
LOAD_WITH: [core/study-creation-core.md]
-->
@@ -31,6 +31,25 @@ This protocol guides you through creating a complete Atomizer optimization study
## Quick Reference
### MANDATORY: Use TodoWrite for Study Creation
**BEFORE creating any files**, add ALL required outputs to TodoWrite:
```
TodoWrite([
{"content": "Create optimization_config.json", "status": "pending", "activeForm": "Creating config"},
{"content": "Create run_optimization.py", "status": "pending", "activeForm": "Creating run script"},
{"content": "Create README.md", "status": "pending", "activeForm": "Creating README"},
{"content": "Create STUDY_REPORT.md", "status": "pending", "activeForm": "Creating report template"}
])
```
**Mark each item complete ONLY after the file is created.** Study is NOT complete until all 4 items are checked off.
> **WHY**: This requirement exists because README.md was forgotten TWICE (2025-12-17, 2026-01-13) despite being listed as mandatory. TodoWrite provides visible enforcement.
---
**Required Outputs** (ALL MANDATORY - study is INCOMPLETE without these):
| File | Purpose | Location | Priority |
|------|---------|----------|----------|
@@ -643,5 +662,6 @@ Generated config:
| Version | Date | Changes |
|---------|------|---------|
| 1.2 | 2026-01-13 | Added MANDATORY TodoWrite requirement for study creation (README forgotten twice) |
| 1.1 | 2025-12-12 | Added FEARunner class pattern, NXSolver initialization warning |
| 1.0 | 2025-12-05 | Initial release |