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>

CLAUDE.md

@@ -93,6 +93,7 @@ The Protocol Operating System (POS) provides layered documentation:
 | Export neural data | OP_05 | `docs/protocols/operations/OP_05_EXPORT_TRAINING_DATA.md` |
 | Debug issues | OP_06 | `docs/protocols/operations/OP_06_TROUBLESHOOT.md` |
 | **Free disk space** | OP_07 | `docs/protocols/operations/OP_07_DISK_OPTIMIZATION.md` |
+| **Generate report** | OP_08 | `docs/protocols/operations/OP_08_GENERATE_REPORT.md` |
 
 ## System Protocols (Technical Specs)
 
@@ -104,6 +105,9 @@ The Protocol Operating System (POS) provides layered documentation:
 | 13 | Dashboard | "dashboard", "real-time", monitoring |
 | 14 | Neural Acceleration | >50 trials, "neural", "surrogate" |
 | 15 | Method Selector | "which method", "recommend", "turbo vs" |
+| 16 | Self-Aware Turbo | "SAT", "turbo v3", high-efficiency optimization |
+| 17 | Study Insights | "insight", "visualization", physics analysis |
+| 18 | Context Engineering | "ACE", "playbook", session context |
 
 **Full specs**: `docs/protocols/system/SYS_{N}_{NAME}.md`
 
@@ -156,8 +160,8 @@ git remote | xargs -L1 git push --all
 Atomizer/
 ├── .claude/skills/           # LLM skills (Bootstrap + Core + Modules)
 ├── docs/protocols/           # Protocol Operating System
-│   ├── operations/           # OP_01 - OP_07
-│   ├── system/              # SYS_10 - SYS_15
+│   ├── operations/           # OP_01 - OP_08
+│   ├── system/              # SYS_10 - SYS_18
 │   └── extensions/          # EXT_01 - EXT_04
 ├── optimization_engine/     # Core Python modules (v2.0)
 │   ├── core/                # Optimization runners, method_selector, gradient_optimizer