docs(zenodo): v6.1 upload summary with inventory (#415)

- Comprehensive file inventory for all 7 bundles + parent collection
- Pre/post-upload checklists for manual workflow
- Bundle-specific upload lists with DOIs
- Figure generation status (14 figures pending)
- Data files status (8 CSV files)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: Antigravity Agent

docs/research/UPLOAD_SUMMARY.md

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+# Zenodo v6.1 Upload Summary
+
+**Date:** 2026-03-26
+**Version:** 6.1
+**Status:** Ready for Upload
+
+φ² + 1/φ² = 3 | TRINITY
+
+---
+
+## Files to Upload per Bundle
+
+### B001: Ternary Neural Networks — HSLM-1.95M Scientific Framework
+**DOI:** 10.5281/zenodo.19227733
+
+| File Type | Files |
+|-----------|-------|
+| **Description** | `zenodo_B001_enhanced_v5.2.md` |
+| **Metadata** | `.zenodo.B001_v6.0.json` |
+| **Figures** | `B001-Fig1_training_curve.png/svg`, `B001-Fig2_format_comparison.png/svg` |
+| **Data** | `B001_training.csv` |
+| **Docker** | `Dockerfile.B001` |
+| **Notebook** | `B001_Training_Analysis.ipynb` |
+
+---
+
+### B002: Zero-DSP FPGA — Pure LUT-Based Ternary Inference
+**DOI:** 10.5281/zenodo.19227735
+
+| File Type | Files |
+|-----------|-------|
+| **Description** | `zenodo_B002_enhanced_v5.2.md` |
+| **Metadata** | `.zenodo.B002_v6.0.json` |
+| **Figures** | `B002-Fig1_fpga_resources.png/svg`, `B002-Fig2_power_analysis.png/svg` |
+| **Data** | `B002_fpga_synthesis.csv` |
+| **Docker** | `Dockerfile.B002` |
+| **Notebook** | `B002_FPGA_Analysis.ipynb` |
+
+---
+
+### B003: TRI-27 ISA — 27-Register Ternary Instruction Set
+**DOI:** 10.5281/zenodo.19227737
+
+| File Type | Files |
+|-----------|-------|
+| **Description** | `zenodo_B003_enhanced_v5.2.md` |
+| **Metadata** | `.zenodo.B003_v6.0.json` |
+| **Figures** | `B003-Fig1_register_layout.png/svg` |
+| **Data** | `B003_tri27_registers.csv` |
+| **Docker** | `Dockerfile.B003` |
+
+---
+
+### B004: Queen Lotus Cycle — Autonomous Learning with Episode Retrieval
+**DOI:** 10.5281/zenodo.19227739
+
+| File Type | Files |
+|-----------|-------|
+| **Description** | `zenodo_B004_enhanced_v5.2.md` |
+| **Metadata** | `.zenodo.B004_v6.0.json` |
+| **Figures** | `B004-Fig1_lotus_cycle.png/svg` |
+| **Data** | `B004_lotus_cycle.csv` |
+| **Docker** | `Dockerfile.B004` |
+
+---
+
+### B005: Tri Language — Linear Types, Effects, Pattern Matching
+**DOI:** 10.5281/zenodo.19227741
+
+| File Type | Files |
+|-----------|-------|
+| **Description** | `zenodo_B005_enhanced_v5.2.md` |
+| **Metadata** | `.zenodo.B005_v6.0.json` |
+| **Figures** | `B005-Fig1_type_hierarchy.png/svg` |
+| **Data** | `B005_language_features.csv` |
+| **Docker** | `Dockerfile.B005` |
+
+---
+
+### B006: Sacred GF16/TF3 — φ-Optimal Number Formats for Ternary
+**DOI:** 10.5281/zenodo.19227743
+
+| File Type | Files |
+|-----------|-------|
+| **Description** | `zenodo_B006_enhanced_v5.2.md` |
+| **Metadata** | `.zenodo.B006_v6.0.json` |
+| **Figures** | `B006-Fig1_gf16_layout.png/svg`, `B006-Fig2_phi_heatmap.png/svg` |
+| **Data** | `B006_gf16_accuracy.csv` |
+| **Docker** | `Dockerfile.B006` |
+| **Notebook** | `B007_VSA_Analysis.ipynb` (shared) |
+
+---
+
+### B007: VSA Operations — HybridBigInt with SIMD Acceleration
+**DOI:** 10.5281/zenodo.19227745
+
+| File Type | Files |
+|-----------|-------|
+| **Description** | `zenodo_B007_enhanced_v5.2.md` |
+| **Metadata** | `.zenodo.B007_v6.0.json` |
+| **Figures** | `B007-Fig1_vsa_structure.png/svg`, `B007-Fig2_simd_speedup.png/svg` |
+| **Data** | `B007_simd_benchmarks.csv`, `B007_noise_resilience.csv` |
+| **Docker** | `Dockerfile.B007` |
+| **Notebook** | `B007_VSA_Analysis.ipynb` |
+
+---
+
+### PARENT: Trinity S³AI Framework Collection
+**DOI:** 10.5281/zenodo.19227879
+
+| File Type | Files |
+|-----------|-------|
+| **Description** | `ZENODO_README.md` |
+| **Metadata** | `.zenodo.parent_v6.0.json` |
+| **Additional** | `CITATION.cff`, `TRINITY_S3AI_UNIFIED_FRAMEWORK.md` |
+
+---
+
+## Upload Instructions
+
+### Option A: Manual Web UI Upload
+
+1. Visit https://zenodo.org/deposit
+2. For each bundle (B001-B007):
+   - **Upload Files:**
+     - Description markdown (drag & drop)
+     - All figures (PNG + SVG)
+     - All data files (CSV)
+     - Dockerfile
+     - Jupyter notebook (if applicable)
+   - **Enter Metadata:**
+     - Copy from `.zenodo.BXXX_v6.0.json`
+     - **IMPORTANT:** Update ORCID from placeholder `0000-0000-0000-0000`
+   - **Click 'Publish'**
+3. For parent collection:
+   - Create new version
+   - Update README with cross-references
+   - Add all child bundle DOIs
+   - Publish
+
+### Option B: Automated API Upload
+
+```bash
+# Set your Zenodo personal access token
+export ZENODO_TOKEN=your_token_here
+
+# Run the upload script
+cd docs/research/figures
+python3 generate_all_figures.py
+cd ..
+python3 ../scripts/upload_zenodo_v6.1.py
+```
+
+---
+
+## Pre-Upload Checklist
+
+### Metadata
+- [ ] Update ORCID in all `.zenodo.BXXX_v6.0.json` files (replace `0000-0000-0000-0000`)
+- [ ] Verify all DOIs match existing Zenodo records
+- [ ] Check keywords include MeSH + ACM CCS terms
+- [ ] Verify related identifiers point to correct cross-references
+
+### Figures
+- [ ] Run `python3 docs/research/figures/generate_all_figures.py`
+- [ ] Verify all PNG files exist (14 figures)
+- [ ] Verify all SVG files exist (14 figures)
+- [ ] Check figures render correctly (open in viewer)
+
+### Data Files
+- [ ] Verify all 8 CSV files are present
+- [ ] Check CSV formatting (no corrupted characters)
+- [ ] Verify data matches published results
+
+### Dockerfiles
+- [ ] Verify all 7 Dockerfiles are syntactically correct
+- [ ] Test build at least one Dockerfile: `docker build -f docs/research/docker/Dockerfile.B001`
+- [ ] Check FROM images use `ziglang/zig:0.15.0-alpine`
+
+### Notebooks
+- [ ] Verify all 3 Jupyter notebooks exist
+- [ ] Test notebooks run without errors
+- [ ] Check notebook outputs are cleared (to reduce file size)
+
+---
+
+## Post-Upload Checklist
+
+### Verification
+- [ ] All DOIs resolve correctly
+- [ ] All files are accessible via download
+- [ ] Metadata displays correctly on Zenodo
+- [ ] Figures render in preview
+
+### Cross-References
+- [ ] Parent collection references all child bundles
+- [ ] Each child bundle references parent collection
+- [ ] Related identifiers are bidirectional
+
+### Documentation
+- [ ] Update `CITATION.cff` with new version
+- [ ] Update `ZENODO_README.md` with v6.1 release notes
+- [ ] Record new DOIs in project README
+
+---
+
+## Figure Generation Status
+
+| Figure | Status | Notes |
+|--------|--------|-------|
+| B001-Fig1_training_curve | Pending | Run notebook/gen script |
+| B001-Fig2_format_comparison | Pending | Run notebook/gen script |
+| B002-Fig1_fpga_resources | Pending | Run notebook/gen script |
+| B002-Fig2_power_analysis | Pending | Run notebook/gen script |
+| B002-Fig3_utilization | Pending | Run notebook/gen script |
+| B003-Fig1_register_layout | Pending | Requires ASCII→PNG |
+| B004-Fig1_lotus_cycle | Pending | Requires diagram |
+| B005-Fig1_type_hierarchy | Pending | Requires diagram |
+| B006-Fig1_gf16_layout | Pending | Run notebook/gen script |
+| B006-Fig2_phi_heatmap | Pending | Run notebook/gen script |
+| B007-Fig1_vsa_structure | Pending | Run notebook/gen script |
+| B007-Fig2_simd_speedup | Pending | Run notebook/gen script |
+| B007-Fig3_noise_resilience | Pending | Run notebook/gen script |
+| B007-Fig4_similarity_distribution | Pending | Run notebook/gen script |
+
+**Total: 14 figures**
+
+---
+
+## Data Files Status
+
+| File | Rows | Status |
+|------|------|--------|
+| B001_training.csv | 7 | ✅ |
+| B002_fpga_synthesis.csv | 4 | ✅ |
+| B003_tri27_registers.csv | 27 | ✅ |
+| B004_lotus_cycle.csv | 5 | ✅ |
+| B005_language_features.csv | 8 | ✅ |
+| B006_gf16_accuracy.csv | 6 | ✅ |
+| B007_simd_benchmarks.csv | 6 | ✅ |
+| B007_noise_resilience.csv | 11 | ✅ |
+
+**Total: 8 data files, 74 rows**
+
+---
+
+## v6.1 Enhancements Summary
+
+### New in v6.0
+- ✅ Standardized MeSH + ACM CCS keywords
+- ✅ ORCID metadata fields (placeholder)
+- ✅ Related identifiers for cross-bundle linking
+- ✅ Figure generation script
+- ✅ 8 CSV data files
+- ✅ 7 Docker reproducibility containers
+- ✅ Enhanced JSON metadata
+
+### New in v6.1
+- ✅ 3 Jupyter analysis notebooks
+- ✅ Algorithm pseudocode documentation
+- ✅ Ablation study results
+- ✅ SOTA comparison tables
+- ✅ Extended mathematical foundations
+- ✅ Video recording scripts
+- ✅ Upload automation script
+- ✅ This comprehensive upload summary
+
+---
+
+## Contact & Support
+
+**Author:** Dmitrii Vasilev
+**Repository:** https://github.com/gHashTag/trinity
+**License:** MIT
+
+For questions or issues, please open a GitHub issue.
+
+---
+
+**φ² + 1/φ² = 3 | TRINITY**