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>

knowledge_base/playbook.json

@@ -0,0 +1,94 @@
+{
+  "version": 1,
+  "last_updated": "2026-01-06T12:00:00",
+  "items": {
+    "str-00001": {
+      "id": "str-00001",
+      "category": "str",
+      "content": "Use TPE sampler for single-objective optimization with <4 design variables",
+      "helpful_count": 5,
+      "harmful_count": 0,
+      "created_at": "2026-01-06T12:00:00",
+      "last_used": null,
+      "source_trials": [],
+      "tags": ["optimization", "sampler"]
+    },
+    "str-00002": {
+      "id": "str-00002",
+      "category": "str",
+      "content": "Use CMA-ES for continuous optimization with 4+ design variables",
+      "helpful_count": 3,
+      "harmful_count": 0,
+      "created_at": "2026-01-06T12:00:00",
+      "last_used": null,
+      "source_trials": [],
+      "tags": ["optimization", "sampler"]
+    },
+    "mis-00001": {
+      "id": "mis-00001",
+      "category": "mis",
+      "content": "Always close NX process when done to avoid zombie processes consuming resources",
+      "helpful_count": 10,
+      "harmful_count": 0,
+      "created_at": "2026-01-06T12:00:00",
+      "last_used": null,
+      "source_trials": [],
+      "tags": ["nx", "process", "critical"]
+    },
+    "mis-00002": {
+      "id": "mis-00002",
+      "category": "mis",
+      "content": "Never trust surrogate predictions with confidence < 0.7 for production trials",
+      "helpful_count": 5,
+      "harmful_count": 0,
+      "created_at": "2026-01-06T12:00:00",
+      "last_used": null,
+      "source_trials": [],
+      "tags": ["surrogate", "validation"]
+    },
+    "cal-00001": {
+      "id": "cal-00001",
+      "category": "cal",
+      "content": "Relative WFE = (WFE_current - WFE_baseline) / WFE_baseline, NOT WFE_baseline / WFE_current",
+      "helpful_count": 3,
+      "harmful_count": 0,
+      "created_at": "2026-01-06T12:00:00",
+      "last_used": null,
+      "source_trials": [],
+      "tags": ["zernike", "calculation", "critical"]
+    },
+    "tool-00001": {
+      "id": "tool-00001",
+      "category": "tool",
+      "content": "Use extract_zernike_figure for surface figure analysis (E20), extract_zernike_opd for optical path difference (E21)",
+      "helpful_count": 4,
+      "harmful_count": 0,
+      "created_at": "2026-01-06T12:00:00",
+      "last_used": null,
+      "source_trials": [],
+      "tags": ["extractor", "zernike"]
+    },
+    "dom-00001": {
+      "id": "dom-00001",
+      "category": "dom",
+      "content": "For mirror optimization: WFE = 2 * surface figure RMS (reflection doubles error)",
+      "helpful_count": 3,
+      "harmful_count": 0,
+      "created_at": "2026-01-06T12:00:00",
+      "last_used": null,
+      "source_trials": [],
+      "tags": ["mirror", "optics", "fundamental"]
+    },
+    "wf-00001": {
+      "id": "wf-00001",
+      "category": "wf",
+      "content": "Always run 5-10 initial FEA trials before enabling surrogate to establish baseline",
+      "helpful_count": 4,
+      "harmful_count": 0,
+      "created_at": "2026-01-06T12:00:00",
+      "last_used": null,
+      "source_trials": [],
+      "tags": ["surrogate", "workflow"]
+    }
+  }
+}