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feat: Implement Agentic Architecture for robust session workflows

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Phase 1 - Session Bootstrap:
- Add .claude/ATOMIZER_CONTEXT.md as single entry point for new sessions
- Add study state detection and task routing

Phase 2 - Code Deduplication:
- Add optimization_engine/base_runner.py (ConfigDrivenRunner)
- Add optimization_engine/generic_surrogate.py (ConfigDrivenSurrogate)
- Add optimization_engine/study_state.py for study detection
- Add optimization_engine/templates/ with registry and templates
- Studies now require ~50 lines instead of ~300

Phase 3 - Skill Consolidation:
- Add YAML frontmatter metadata to all skills (versioning, dependencies)
- Consolidate create-study.md into core/study-creation-core.md
- Update 00_BOOTSTRAP.md, 01_CHEATSHEET.md, 02_CONTEXT_LOADER.md

Phase 4 - Self-Expanding Knowledge:
- Add optimization_engine/auto_doc.py for auto-generating documentation
- Generate docs/generated/EXTRACTORS.md (27 extractors documented)
- Generate docs/generated/TEMPLATES.md (6 templates)
- Generate docs/generated/EXTRACTOR_CHEATSHEET.md

Phase 5 - Subagent Implementation:
- Add .claude/commands/study-builder.md (create studies)
- Add .claude/commands/nx-expert.md (NX Open API)
- Add .claude/commands/protocol-auditor.md (config validation)
- Add .claude/commands/results-analyzer.md (results analysis)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
Antoine
2025-12-07 14:52:25 -05:00
parent 6cf12d9344
commit 0e04457539
22 changed files with 4708 additions and 2212 deletions
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23
.claude/skills/00_BOOTSTRAP.md
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@@ -1,6 +1,16 @@
---
skill_id: SKILL_000
version: 2.0
last_updated: 2025-12-07
type: bootstrap
code_dependencies: []
requires_skills: []
---
# Atomizer LLM Bootstrap
**Version**: 1.0
**Version**: 2.0
**Updated**: 2025-12-07
**Purpose**: First file any LLM session reads. Provides instant orientation and task routing.
---
@@ -61,7 +71,7 @@ User Request
| User Intent | Keywords | Protocol | Skill to Load | Privilege |
|-------------|----------|----------|---------------|-----------|
| Create study | "new", "set up", "create", "optimize" | OP_01 | **create-study-wizard.md** | user |
| Create study | "new", "set up", "create", "optimize" | OP_01 | **core/study-creation-core.md** | user |
| Run optimization | "start", "run", "execute", "begin" | OP_02 | - | user |
| Monitor progress | "status", "progress", "trials", "check" | OP_03 | - | user |
| Analyze results | "results", "best", "compare", "pareto" | OP_04 | - | user |
@@ -107,15 +117,14 @@ See `02_CONTEXT_LOADER.md` for complete loading rules.
**Quick Reference**:
```
CREATE_STUDY → create-study-wizard.md (PRIMARY)
→ Use: from optimization_engine.study_wizard import StudyWizard, create_study
→ modules/extractors-catalog.md (if asks about extractors)
CREATE_STUDY → core/study-creation-core.md (PRIMARY)
→ SYS_12_EXTRACTOR_LIBRARY.md (extractor reference)
→ modules/zernike-optimization.md (if telescope/mirror)
→ modules/neural-acceleration.md (if >50 trials)
RUN_OPTIMIZATION → OP_02_RUN_OPTIMIZATION.md
→ SYS_10_IMSO.md (if adaptive)
→ SYS_13_DASHBOARD_TRACKING.md (if monitoring)
→ SYS_15_METHOD_SELECTOR.md (method recommendation)
→ SYS_14_NEURAL_ACCELERATION.md (if neural/turbo)
DEBUG → OP_06_TROUBLESHOOT.md
→ Relevant SYS_* based on error type