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Anto01 b8a04c62b8 docs: Consolidate documentation and fix protocol numbering (partial)

Phase 2 of restructuring plan:
- Rename SYS_16_STUDY_INSIGHTS -> SYS_17_STUDY_INSIGHTS
- Rename SYS_17_CONTEXT_ENGINEERING -> SYS_18_CONTEXT_ENGINEERING
- Promote Bootstrap V3.0 (Context Engineering) as default
- Archive old Bootstrap V2.0
- Create knowledge_base/playbook.json for ACE framework
- Add OP_08 (Generate Report) to routing tables
- Add SYS_16-18 to protocol tables
- Update docs/protocols/README.md to version 1.1
- Update CLAUDE.md with new protocols
- Create docs/plans/RESTRUCTURING_PLAN.md for continuation

Remaining: Phase 2.8 (Cheatsheet), Phases 3-6

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

2026-01-07 08:52:07 -05:00

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Physics Documentation Index

This folder contains detailed physics and domain-specific documentation for Atomizer's analysis capabilities. These documents explain the engineering and scientific foundations behind the extractors and insights.

Document Catalog

Document	Topic	When to Read
ZERNIKE_FUNDAMENTALS.md	Zernike polynomial basics, RMS calculation, multi-subcase analysis	Setting up mirror optimization, understanding WFE metrics
ZERNIKE_OPD_METHOD.md	Rigorous OPD method for lateral displacement correction	Lateral support optimization, validating WFE accuracy

For Mirror/Optics Optimization

New to Zernike? Start with ZERNIKE_FUNDAMENTALS.md
Lateral support optimization? Read ZERNIKE_OPD_METHOD.md - critical
Mid-spatial frequency analysis? See SYS_16 (msf_zernike insight)

For Structural Optimization

Stress extraction: See SYS_12_EXTRACTOR_LIBRARY.md (E3, E12)
Strain energy: See SYS_12_EXTRACTOR_LIBRARY.md (E13)

For Thermal Analysis

Temperature extraction: See SYS_12_EXTRACTOR_LIBRARY.md (E15-E17)

Location	Content
`.claude/skills/modules/extractors-catalog.md`	Quick extractor lookup
`.claude/skills/modules/insights-catalog.md`	Quick insight lookup
`docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md`	Extractor specifications
`docs/protocols/system/SYS_17_STUDY_INSIGHTS.md`	Insight specifications

Contributing Physics Documentation

When adding new physics documentation:

Naming: Use {TOPIC}_{SUBTOPIC}.md format (e.g., THERMAL_GRADIENTS.md)
Structure: Follow the pattern in existing documents:
- Executive Summary
- Mathematical Formulation
- When This Matters
- Implementation Details
- Usage Guide
- Validation
Cross-reference: Update this index and related skill modules
Link to code: Reference the implementing extractors/insights

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