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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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62
.claude/settings.local.json
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@@ -21,25 +21,51 @@
"Bash(curl:*)",
"Read",
"Skill(dashboard:*)",
"Bash(C:Usersantoianaconda3envsatomizerpython.exe:*)",
"Bash(del \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_flat_back_V5\\\\3_results\\\\study.db\")",
"Bash(C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe -c:*)",
"Bash(C:Usersantoianaconda3envsatomizerpython.exe run_optimization.py --trials 1)",
"Bash(C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe -m py_compile:*)",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver analyze \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\")",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_V12\")",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_V2\")",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_V11\")",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_V11\" --execute)",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_flat_back_V3\")",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_flat_back_V3\" --execute)",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_flat_back_V6\" --execute)",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_flat_back_V1\" --execute)",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_flat_back_V5\" --execute)",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction_V12\" --execute)",
"Bash(\"C:\\\\Users\\\\antoi\\\\anaconda3\\\\envs\\\\atomizer\\\\python.exe\" -m optimization_engine.utils.study_archiver cleanup \"C:\\\\Users\\\\antoi\\\\Atomizer\\\\studies\\\\M1_Mirror\\\\m1_mirror_cost_reduction\" --execute)"
"Bash(C:/Users/antoi/anaconda3/envs/atomizer/python.exe:*)",
"Bash(C:\\Users\\antoi\\anaconda3\\envs\\atomizer\\python.exe:*)",
"Bash(\"C:\\Users\\antoi\\anaconda3\\envs\\atomizer\\python.exe\":*)",
"Bash(ls:*)",
"Bash(mkdir:*)",
"Bash(timeout:*)",
"Bash(sqlite3:*)",
"Bash(bash:*)",
"Bash(sh:*)",
"Skill(ralph-wiggum:ralph-loop)",
"Skill(ralph-wiggum:ralph-loop:*)",
"Skill(ralph-wiggum:help)",
"Skill(ralph-wiggum:help:*)",
"Skill(study-builder)",
"Skill(study-builder:*)",
"Bash(cat:*)",
"Bash(du:*)",
"Bash(for file in docs/protocols/operations/OP_*.md)",
"Bash(do basename \"$file\")",
"Bash(done)",
"Bash(for file in docs/protocols/system/SYS_*.md)",
"Bash(for file in docs/protocols/extensions/EXT_*.md)",
"Bash(grep:*)",
"Bash(wc:*)",
"Bash(.claude/skills/00_BOOTSTRAP.md )",
"Bash(.claude/skills/00_BOOTSTRAP_V2.md )",
"Bash(.claude/skills/archive/00_BOOTSTRAP_V2.0_archived.md )",
"Bash(.claude/skills/01_CHEATSHEET.md )",
"Bash(.claude/skills/modules/OPTIMIZATION_ENGINE_MIGRATION_PLAN.md )",
"Bash(.claude/skills/modules/insights-catalog.md )",
"Bash(CLAUDE.md )",
"Bash(docs/06_PHYSICS/ )",
"Bash(docs/api/CONTEXT_ENGINEERING_API.md )",
"Bash(docs/protocols/ )",
"Bash(knowledge_base/playbook.json )",
"Bash(docs/plans/RESTRUCTURING_PLAN.md)",
"Bash(.claude/skills/archive/ )",
"Bash(C:Usersantoianaconda3envsatomizerpython.exe -m uvicorn:*)",
"Bash(xargs -I{} git ls-tree -r -l HEAD {})",
"Bash(sort:*)",
"Bash(C:Usersantoianaconda3envsatomizerpython.exe introspect_model.py)",
"Bash(xargs:*)"
],
"deny": [],
"ask": []
}
},
"enableAllProjectMcpServers": true
}