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>

docs/06_PHYSICS/00_INDEX.md

@@ -39,7 +39,7 @@ This folder contains detailed physics and domain-specific documentation for Atom
 | `.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_16_STUDY_INSIGHTS.md` | Insight specifications |
+| `docs/protocols/system/SYS_17_STUDY_INSIGHTS.md` | Insight specifications |
 
 ---
 

docs/06_PHYSICS/ZERNIKE_FUNDAMENTALS.md

@@ -315,7 +315,7 @@ studies/
 ### Protocol Documentation
 
 - `docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md` - Extractor specifications (E8-E10: Standard Zernike, E20-E21: OPD method)
-- `docs/protocols/system/SYS_16_STUDY_INSIGHTS.md` - Insight specifications (`zernike_wfe`, `zernike_opd_comparison`)
+- `docs/protocols/system/SYS_17_STUDY_INSIGHTS.md` - Insight specifications (`zernike_wfe`, `zernike_opd_comparison`)
 
 ### Skill Modules (Quick Lookup)
 

docs/06_PHYSICS/ZERNIKE_OPD_METHOD.md

@@ -558,7 +558,7 @@ The `concave` parameter in the code handles this sign flip.
 | `.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 (E8-E10, E20-E21) |
-| `docs/protocols/system/SYS_16_STUDY_INSIGHTS.md` | Insight specifications |
+| `docs/protocols/system/SYS_17_STUDY_INSIGHTS.md` | Insight specifications |
 
 ---