docs(zenodo): V6.3 improvement proposal + bundle dependency graph (#435)

- Gap analysis: v6.2 vs best practices
- Priority 1: ORCID integration, related identifiers
- Priority 2: Video demos, analysis notebooks, dependency graph
- Priority 3: Automated upload, conference templates
- Bundle dependency graph (PNG + SVG + DOT)

Timeline: ~20-25 hours for v6.3 completion

φ² + 1/φ² = 3 | TRINITY

Author: Antigravity Agent

docs/research/ZENODO_V6.3_IMPROVEMENT_PROPOSAL.md

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+# Zenodo v6.3 Improvement Proposal
+
+**Date:** 2026-03-27  
+**Based on:** ZENODO_PUBLICATION_BEST_PRACTICES_2026_COMPREHENSIVE.md  
+**Current Version:** v6.2.0
+
+---
+
+## Gap Analysis: v6.2 vs Best Practices
+
+### Priority 1: Critical Gaps (Must Fix)
+
+#### 1. ORCID Integration
+**Status:** Placeholder value `0000-0000-0000-0000`  
+**Required:** Real ORCID from author  
+**Impact:** Zenodo 2026 requirement, citation tracking
+
+**Action:** Update all 8 JSON files with real ORCID
+
+```json
+"creators": [
+  {
+    "name": "Vasilev, Dmitrii",
+    "orcid": "0000-0002-XXXX-XXXX",  // USER TO PROVIDE
+    "affiliation": "Independent Researcher"
+  }
+]
+```
+
+#### 2. Related Identifiers
+**Status:** Partially implemented  
+**Missing:** Cross-bundle references, arXiv links
+
+**Action:** Add to each bundle:
+```json
+"related_identifiers": [
+  {
+    "scheme": "doi",
+    "identifier": "10.5281/zenodo.19227879",
+    "relation": "isPartOf",
+    "resource_type": "publication"
+  },
+  {
+    "scheme": "url",
+    "identifier": "https://github.com/gHashTag/trinity",
+    "relation": "isSupplementedBy"
+  }
+]
+```
+
+### Priority 2: Enhancement Opportunities
+
+#### 3. Video Demonstrations
+**Status:** Not recorded  
+**Recommendation:** 2-5 min demos for key bundles
+
+**Priority Order:**
+1. B001 HSLM — Training demo with loss curve
+2. B002 FPGA — Synthesis + resource usage
+3. B005 VIBEE — Code generation workflow
+
+**Script Template:**
+- 0:00-0:05 — Title slide
+- 0:05-0:30 — Architecture overview
+- 0:30-2:30 — Code demonstration
+- 2:30-3:00 — Results/metrics
+- 3:00-3:05 — Citation/DOI
+
+#### 4. Supplementary Analysis Notebooks
+**Status:** CSV data exported, no analysis scripts  
+**Recommendation:** Jupyter notebooks for reproducible analysis
+
+**Create:**
+- `B001_Training_Analysis.ipynb` — Load CSV, plot curves, compute stats
+- `B007_VSA_Analysis.ipynb` — Noise resilience visualization
+- `B002_FPGA_Analysis.ipynb` — Resource comparison plots
+
+#### 5. Cross-Bundle Dependency Graph
+**Status:** Text description only  
+**Recommendation:** Visual dependency graph
+
+**Create:** `docs/research/figures/bundle_dependencies.svg`
+
+```
+PARENT (Trinity S³AI)
+├── B001 (HSLM) ────────┐
+├── B002 (FPGA) ────────┤
+├── B003 (TRI-27) ──────┤
+├── B004 (Lotus) ───────┼──► Applications
+├── B005 (VIBEE) ───────┤
+├── B006 (Sacred) ──────┤
+└── B007 (VSA) ─────────┘
+```
+
+### Priority 3: Nice to Have
+
+#### 6. Automated Zenodo Upload
+**Status:** Manual Web UI  
+**Recommendation:** GitHub Actions workflow
+
+```yaml
+# .github/workflows/zenodo-publish.yml
+name: Zenodo Auto-Publish
+on:
+  release:
+    types: [published]
+jobs:
+  zenodo:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: zenodo/zenodo-upload-github@main
+```
+
+#### 7. Conference-Specific Templates
+**Status:** Generic descriptions  
+**Recommendation:** NeurIPS/ICLR/MLSys specific abstracts
+
+**Create:**
+- `docs/research/submissions/neurips2026/abstract.md`
+- `docs/research/submissions/iclr2027/abstract.md`
+- `docs/research/submissions/mlsys2025/abstract.md`
+
+---
+
+## Proposed v6.3 Timeline
+
+### Week 1: Critical Fixes (3-4 hours)
+- [ ] Update ORCID in all 8 JSON files
+- [ ] Add related identifiers to all bundles
+- [ ] Validate JSON schemas
+
+### Week 2: Enhanced Assets (8-10 hours)
+- [ ] Record 3 video demos (B001, B002, B005)
+- [ ] Create 3 Jupyter analysis notebooks
+- [ ] Generate bundle dependency graph
+
+### Week 3: Conference Templates (4-6 hours)
+- [ ] Write NeurIPS 2026 abstract
+- [ ] Write ICLR 2027 abstract
+- [ ] Write MLSys 2025 abstract
+
+### Week 4: Release (2-3 hours)
+- [ ] Create GitHub release v6.3.0
+- [ ] Upload to Zenodo (8 depositions)
+- [ ] Submit to conferences
+
+**Total: ~20-25 hours**
+
+---
+
+## Success Criteria for v6.3
+
+1. ✅ ORCID integrated (real value)
+2. ✅ Cross-bundle references established
+3. ✅ At least 3 video demos recorded
+4. ✅ At least 3 analysis notebooks created
+5. ✅ Visual dependency graph
+6. ✅ Conference-specific abstracts
+7. ✅ All FAIR principles met (15/15)
+
+---
+
+## v6.3 File Inventory (Projected)
+
+| Category | v6.2 | v6.3 | Delta |
+|----------|------|------|-------|
+| Markdown descriptions | 8 | 8 | — |
+| JSON metadata | 8 | 8 | — |
+| Figures (PNG+SVG) | 28 | 30 | +2 |
+| Data files (CSV) | 10 | 10 | — |
+| Dockerfiles | 7 | 7 | — |
+| Video demos | 0 | 3 | +3 |
+| Jupyter notebooks | 0 | 3 | +3 |
+| Conference abstracts | 0 | 3 | +3 |
+| **Total** | **61** | **72** | **+11** |
+
+---
+
+**φ² + 1/φ² = 3 | TRINITY**

docs/research/figures/bundle_dependencies.dot

@@ -0,0 +1,58 @@
+digraph TrinityBundles {
+    // Trinity S³AI Bundle Dependency Graph
+    // Generated: 2026-03-27
+    // φ² + 1/φ² = 3
+    
+    rankdir=TB;
+    node [fontname="Arial", fontsize=12];
+    edge [fontname="Arial", fontsize=10];
+    
+    // Parent Collection
+    PARENT [label="Trinity S³AI\n(PARENT)", shape=box, style=filled, fillcolor="#FFD700", fontsize=14, fontweight=bold];
+    
+    // Core Bundles
+    B001 [label="B001: HSLM\n(Hierarchical Sacred\nLanguage Model)", shape=box, style=filled, fillcolor="#87CEEB"];
+    B002 [label="B002: FPGA\n(Zero-DSP\nImplementation)", shape=box, style=filled, fillcolor="#87CEEB"];
+    B003 [label="B003: TRI-27\n(Ternary ISA)", shape=box, style=filled, fillcolor="#87CEEB"];
+    B004 [label="B004: Lotus\n(Orchestration)", shape=box, style=filled, fillcolor="#98FB98"];
+    B005 [label="B005: VIBEE\n(Code Generator)", shape=box, style=filled, fillcolor="#98FB98"];
+    B006 [label="B006: Sacred\n(Formats & Math)", shape=box, style=filled, fillcolor="#DDA0DD"];
+    B007 [label="B007: VSA\n(Vector Symbolic\nArchitecture)", shape=box, style=filled, fillcolor="#DDA0DD"];
+    
+    // Applications Layer
+    APPLICATIONS [label="Applications\n(Trinity Apps)", shape=ellipse, style=filled, fillcolor="#FFB6C1", fontsize=14];
+    
+    // Dependencies
+    PARENT -> B001 [label="contains"];
+    PARENT -> B002 [label="contains"];
+    PARENT -> B003 [label="contains"];
+    PARENT -> B004 [label="contains"];
+    PARENT -> B005 [label="contains"];
+    PARENT -> B006 [label="contains"];
+    PARENT -> B007 [label="contains"];
+    
+    // Inter-bundle dependencies
+    B001 -> B002 [label="deploys to", style=dashed];
+    B001 -> B003 [label="compiles to", style=dashed];
+    B003 -> B002 [label="synthesizes", style=dashed];
+    B005 -> B003 [label="generates", style=dashed];
+    B005 -> B002 [label="generates", style=dashed];
+    B006 -> B001 [label="formats", style=dashed];
+    B007 -> B001 [label="enhances", style=dashed];
+    
+    // Application dependencies
+    B001 -> APPLICATIONS [label="models in"];
+    B002 -> APPLICATIONS [label="runs on"];
+    B003 -> APPLICATIONS [label="executes on"];
+    B004 -> APPLICATIONS [label="orchestrates"];
+    B005 -> APPLICATIONS [label="builds"];
+    B006 -> APPLICATIONS [label="serializes"];
+    B007 -> APPLICATIONS [label="reasons in"];
+    
+    // Legend
+    {rank=same; B001 B002 B003}
+    {rank=same; B004 B005 B006 B007}
+    
+    label="Trinity S³AI Bundle Dependency Graph\nφ² + 1/φ² = 3";
+    fontsize=10;
+}