hummbl-bibliography 1.0.0

package/README.md

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+# HUMMBL Bibliography
+
+![Total Entries](https://img.shields.io/badge/entries-240-blue)
+![DOI Coverage](https://img.shields.io/badge/DOIs-65%25-yellow)
+![ISBN Coverage](https://img.shields.io/badge/ISBNs-30%25-green)
+![Abstract Coverage](https://img.shields.io/badge/abstracts-100%25-brightgreen)
+![Validation](https://github.com/hummbl-dev/hummbl-bibliography/workflows/validate/badge.svg)
+
+A production-ready bibliography management system for the **HUMMBL (Base120) cognitive framework**. This repository maintains 240 curated academic and practitioner works organized into 12 thematic tiers, mapped to 6 cognitive transformations.
+
+## 🎯 Overview
+
+The HUMMBL cognitive framework identifies six fundamental thinking operations:
+
+- **P** (Perspective/Identity): Frame and name what is. Anchor or shift point of view.
+- **IN** (Inversion): Reverse assumptions. Examine opposites, edges, negations.
+- **CO** (Composition): Combine parts into coherent wholes.
+- **DE** (Decomposition): Break complex systems into constituent parts.
+- **RE** (Recursion): Apply operations iteratively, with outputs becoming inputs.
+- **SY** (Meta-Systems): Understand systems of systems, coordination, and emergent dynamics.
+
+This bibliography provides the theoretical foundation and empirical evidence for these transformations through carefully selected works spanning systems thinking, cognitive psychology, design, and organizational learning.
+
+## 📚 Bibliography Structure
+
+### Twelve Thematic Tiers (20 entries each)
+
+| Tier | Domain | Examples |
+|------|--------|----------|
+| **T1: Canonical** | Foundational theoretical works | Meadows, Kahneman, Simon, Pearl |
+| **T2: Empirical** | Peer-reviewed research | Tversky & Kahneman, Klein, Gigerenzer |
+| **T3: Applied** | Practitioner texts | Lean Startup, Design Thinking, DevOps |
+| **T4: Agentic** | AI safety & multi-agent systems | Russell, Amodei, Constitutional AI |
+| **T5: Engineering** | Software patterns for agents | Circuit breakers, stigmergy, BDI, DbC |
+| **T6: Governance** | AI regulation & assurance | EU AI Act, NIST RMF, OWASP LLM Top 10 |
+| **T7: Emerging** | Cutting-edge agent research | ReAct, CoT, RAG, SWE-bench, ToT |
+| **T8: Cognition** | Mental models & knowledge | Craik, Piaget, Zettelkasten, CoP |
+| **T9: Economics** | AI economics & platforms | Coase, Tirole, scaling laws, auctions |
+| **T10: Collaboration** | Human-AI teaming | Licklider, CSCW, shared mental models |
+| **T11: Security** | Adversarial ML & defense | Goodfellow, zero trust, formal verification |
+| **T12: Complexity** | Complex adaptive systems | Holland, Kauffman, networks, cybernetics |
+
+All 240 entries have abstracts (150-300 words) and HUMMBL transformation tags.
+
+## 🚀 Quick Start
+
+### Clone and Install
+
+```bash
+# Clone the repository
+git clone https://github.com/hummbl-dev/hummbl-bibliography.git
+cd hummbl-bibliography
+
+# Install toolkit dependencies
+cd toolkit
+npm install
+
+# Validate bibliography
+npm run validate
+
+# View statistics
+npm run stats
+```
+
+### Basic Usage
+
+```bash
+# Validate all bibliography files
+npm run validate
+
+# Check for duplicates
+npm run check-dups
+
+# Generate statistics report
+npm run stats
+
+# Extract HUMMBL transformation keywords
+npm run keywords
+
+# Find missing DOIs
+npm run find-dois
+
+# Run full test suite
+npm test
+```
+
+## 📊 Current Metrics
+
+Based on latest analysis (April 2026):
+
+- **Total Entries**: 240 unique works across 12 tiers
+- **Transformation Coverage** (tag count across all entries):
+  - SY (Synthesis): 152
+  - CO (Composition): 115
+  - DE (Decomposition): 103
+  - RE (Recursion): 97
+  - IN (Inversion): 90
+  - P (Perspective): 80
+- **Quality Metrics**:
+  - 100% have abstracts (150-300 word scholarly annotations)
+  - 100% have HUMMBL transformation mappings
+  - 65% have DOIs (155/240)
+  - 30% have ISBNs (72/240)
+  - 0 validation errors, 0 duplicates
+
+## 🔄 HUMMBL Transformation Mapping
+
+Each bibliography entry is tagged with one or more HUMMBL transformations based on its primary cognitive contributions:
+
+```bibtex
+@book{Meadows2008ThinkingSystems,
+  title = {Thinking in Systems: A Primer},
+  author = {Meadows, Donella H.},
+  year = {2008},
+  publisher = {Chelsea Green Publishing},
+  isbn = {978-1603580557},
+  abstract = {...},
+  keywords = {systems thinking, HUMMBL:SY, HUMMBL:RE, HUMMBL:CO}
+}
+```
+
+For detailed guidance on mapping new entries, see [docs/TRANSFORMATION_GUIDE.md](docs/TRANSFORMATION_GUIDE.md).
+
+## 🛠️ Toolkit
+
+The repository includes a comprehensive Node.js toolkit for bibliography management:
+
+| Script | Purpose |
+|--------|---------|
+| `validate.js` | Full validation with error/warning reports |
+| `check-duplicates.js` | Cross-file duplicate detection |
+| `fix-duplicates.js` | Automatic duplicate removal |
+| `find-missing-dois.js` | DOI enrichment via CrossRef API |
+| `stats.js` | Analytics dashboard with transformation coverage |
+| `extract-keywords.js` | HUMMBL transformation keyword extraction |
+| `merge-entries.js` | Interactive entry consolidation |
+
+See [toolkit/README.md](toolkit/README.md) for detailed documentation.
+
+## 📖 Documentation
+
+- [CONTRIBUTING.md](docs/CONTRIBUTING.md) - How to propose new entries
+- [TRANSFORMATION_GUIDE.md](docs/TRANSFORMATION_GUIDE.md) - HUMMBL transformation mapping guidelines
+- [QUALITY_STANDARDS.md](docs/QUALITY_STANDARDS.md) - Citation and metadata standards
+- [GAP_ANALYSIS.md](docs/GAP_ANALYSIS.md) - Current coverage gaps and priorities
+
+## 🤝 Contributing
+
+We welcome contributions! To add a new bibliography entry:
+
+1. Check [docs/GAP_ANALYSIS.md](docs/GAP_ANALYSIS.md) for priority areas
+2. Use the [new-entry issue template](.github/ISSUE_TEMPLATE/new-entry.md)
+3. Follow [QUALITY_STANDARDS.md](docs/QUALITY_STANDARDS.md) for formatting
+4. Map to appropriate HUMMBL transformations
+5. Submit a pull request
+
+All submissions are automatically validated via pre-commit hooks and CI/CD.
+
+## 🔍 Gap Analysis
+
+Current priorities for quality improvement:
+
+- **Perspective (P)**: 80 tags (11.8%) -- underrepresented vs. 16.7% ideal
+- **Inversion (IN)**: 90 tags (13.8%) -- slightly below target
+- **DOI coverage**: 65% overall; T3 (applied/trade books) at 0%
+- **ISBN coverage**: Strong in T1/T3 but low in T4-T12
+
+See [docs/GAP_ANALYSIS.md](docs/GAP_ANALYSIS.md) for detailed analysis.
+
+## 🤖 Automation
+
+### Pre-commit Hooks
+
+Automatically runs validation on modified `.bib` files:
+
+```bash
+cd toolkit
+npm run setup
+```
+
+### GitHub Actions
+
+- **Validation**: Runs on every PR
+- **Stats Report**: Generated weekly
+- **DOI Enrichment**: Manual trigger for batch updates
+
+## 📝 Citation Format
+
+To cite this bibliography:
+
+```bibtex
+@misc{hummbl-bibliography,
+  title = {HUMMBL Bibliography: Curated Works on Cognitive Transformations},
+  author = {{HUMMBL Team}},
+  year = {2025},
+  howpublished = {\url{https://github.com/hummbl-dev/hummbl-bibliography}},
+  note = {Version 1.0}
+}
+```
+
+## 📄 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## 🙏 Acknowledgments
+
+Special thanks to the researchers, authors, and practitioners whose work forms the foundation of the HUMMBL cognitive framework.
+
+---
+
+**Maintained by**: HUMMBL Team  
+**Last Updated**: 2026-04-08  
+**Version**: 2.0.0

package/SECURITY.md

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+# Security Policy
+
+## Reporting a Vulnerability
+
+If you discover a security issue in HUMMBL Bibliography or its toolkit, email `reuben@hummbl.io` with:
+
+- affected file or script
+- reproduction steps
+- expected and observed behavior
+- potential impact
+
+Do not open public GitHub issues for suspected vulnerabilities.
+
+## Scope
+
+This policy covers the bibliography data, validation toolkit, and release artifacts in this repository.

package/SITREP.md

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+# SITREP: HUMMBL Bibliography Repository
+
+**Generated**: 2026-04-09
+**Location**: `PROJECTS/hummbl-bibliography/`
+
+---
+
+## Current Status
+
+### Repository Health
+- **Validation**: 0 errors, 21 warnings (all warnings are missing DOIs/ISBNs)
+- **Duplicates**: 0 (resolved 9 cross-tier duplicates in this audit)
+- **Pre-commit Hooks**: Configured and active
+- **CI/CD**: GitHub Actions workflow operational
+
+### Corpus Metrics
+- **Total Entries**: 240 (12 tiers x 20 entries)
+- **DOI Coverage**: 155/240 (64.6%)
+- **ISBN Coverage**: 72/240 (30%)
+- **Abstract Coverage**: 240/240 (100%)
+- **HUMMBL Keyword Coverage**: 240/240 (100%)
+
+| Metric | Value |
+|--------|-------|
+| Total entries | **260** (20 × 13 tiers) |
+| Tiers | 13 (T1–T13) |
+| Entries with DOIs | ~142 (~55% overall) |
+| T7 DOI coverage | **20/20 (100%)** |
+| T13 DOI coverage | **13/20 (65%)** (arXiv papers) |
+| T1 DOI coverage | 6/20 (30%) |
+| T3 DOI coverage | 0/20 (all trade books; annotated) |
+| T5 DOI coverage | 7/20 (35%) |
+| Cross-tier duplicates | 0 (resolved Apr 2026) |
+| Validation errors | 0 |
+| Abstract coverage | 100% |
+| HUMMBL keyword coverage | 100% |
+| NIST AI RMF tags | 60 entries (T4/T6/T11) |
+| EU AI Act article tags | 60 entries (T4/T6/T11) |
+| ARCANA lenses mapped | 28/28 |
+| BKI propositions mapped | 4/4 |
+
+---
+
+## Recent Changes (v1.3.0 — Apr 2026)
+
+### ✅ T13: Post-2024 Reasoning Models (new tier, 20 entries)
+`bibliography/T13_reasoning.bib` added. Covers o1/o3/o1-mini, DeepSeek-R1/R1-Zero,
+test-time compute scaling, PRMs, STAR/Self-Refine/Self-Consistency, Tree of Thoughts,
+RouteLLM, Claude/Gemini model cards, JudgeBench, AlphaCode 2. 13/20 entries have arXiv DOIs.
+
+### ✅ NIST AI RMF + EU AI Act Crosswalk Tags
+60 entries across T4/T6/T11 now carry `nist_functions` and `eu_ai_act_articles` fields.
+Query: `node toolkit/src/query.js --nist-function GOVERN` returns 60 targeted entries.
+
+### ✅ ARCANA Citation Map (28 lenses)
+`mappings/arcana_citations.json` — all 28 ARCANA philosophical lenses mapped to bibliography
+keys with `primary`, `secondary`, and `gaps` arrays. Critical gaps documented.
+
+### ✅ BKI Evidence Audit
+`mappings/bki_evidence.json` — 4 BKI propositions mapped with coverage grades.
+Overall grade B-. Critical missing: `Edmondson1999PsychologicalSafety`.
+
+### ✅ Open Brain Ingest Script
+`scripts/ingest_to_open_brain.py` — stdlib-only; `--dry-run` (default) or `--post` to live.
+
+### ✅ llms.txt Updated to 260 entries
+AI-readable index regenerated to include T13; now 1,100+ lines.
+
+### ✅ DOI Audit: All 240 pre-T13 Entries Complete
+Full `% No DOI available` annotation pass across T1/T2/T4/T5/T6/T8/T9/T10/T11/T12.
+4 verified DOIs added (CrossRef-confirmed). Overall DOI coverage: ~55%.
+
+### Round 1: Critical Fixes
+- Fixed 4 validation errors (malformed DOI, wrong entry type, 2 dup keys)
+- Resolved 9 duplicate entries across tiers (5 unique conflicts)
+- Fixed 2 wrong DOI assignments (Klein1993, Yao2023TreeOfThoughts)
+- Fixed Patil2023Gorilla wrong arXiv URL
+- Replaced 4 removed duplicates with new entries (Ngo2024, Bengio2024, Sumers2024, Zhuge2024)
+
+### Round 2: Metadata Enrichment
+- Added 10 arXiv DOIs to T7_emerging (now at 100% DOI coverage)
+- Added 10 ISBNs to T8, T9, T12 book entries
+- DOI coverage: 145 -> 155; ISBN coverage: 62 -> 72
+
+### Round 3: Quality Improvement
+- Expanded 5 shallow T3 abstracts from book-jacket to scholarly quality
+- Rebalanced transformation tags: P +5, IN +2, SY -6
+
+### Round 4: Tooling Fix
+- Converted extract-keywords.js from CJS to ESM (was broken)
+- All toolkit scripts now operational
+
+### Round 5: Documentation
+- Updated README.md (was referencing 48 entries / 3 tiers)
+- Updated GAP_ANALYSIS.md (full rewrite from 48-entry analysis)
+- Updated SITREP.md (this document)
+
+---
+
+## Toolkit Status
+
+| Tier | Focus | Highlights |
+|------|-------|------------|
+| T1 | Canonical Foundations | Kahneman, Simon, Pearl, Norman, Miller, Kuhn with DOIs; 6 pre-2000 books annotated |
+| T2 | Empirical Research | Academic journals; most should have DOIs — audit pending |
+| T3 | Applied Practitioner | All 20 trade books annotated with `% No DOI available` |
+| T4 | Governance & Ethics | AI policy, fairness, accountability literature |
+| T5 | Engineering Patterns | 7 DOIs; blog posts (martinfowler.com, LinkedIn) need annotation |
+| T6 | Philosophy of Mind | Phenomenology, embodied cognition, consciousness |
+| T7 | Emerging AI Research | **100% DOI coverage**; all arXiv DOIs present; 3 bugs fixed |
+| T8 | Cognition & Learning | Learning theory, memory, metacognition |
+| T9 | Economics & Incentives | FrugalGPT (canonical home), scaling laws, market design |
+| T10 | Collaboration & Teams | Team dynamics, organizational design, coordination |
+| T11 | Security & Trust | Adversarial ML, threat modeling, trust systems |
+| T12 | Complexity Science | Complex adaptive systems, emergence, network theory |
+| T13 | Post-2024 Reasoning Models | o1/o3/R1-class, test-time compute, PRMs, self-improvement; 65% DOI coverage |
+
+---
+
+## Remaining Priorities
+
+### 🔴 High Priority
+1. ~~**T5 blog post annotations**~~ — ✅ Done (all 4 annotated: Kreps, Fowler, Young, Mahdavi)
+2. ~~**DOI audit for T2, T4, T6, T8–T12**~~ — ✅ Done (v1.3.0)
+3. ~~**T13 evaluation**~~ — ✅ Done (T13_reasoning.bib, 20 entries)
+4. **Verify zero cross-tier duplicates** — run `npm run check-duplicates` after PR #27 merge
+
+### 🟡 Medium Priority
+1. **Bibliography gap fills** — add missing ARCANA critical entries (Weber, Bourdieu, Burnham, Chomsky, Gramsci) and BKI gap (Edmondson1999PsychologicalSafety)
+2. **Watch mode** — `scripts/watch-bib.js` for hot-reload citation updates (issue #36)
+3. **Citation graph** — D3.js/Mermaid visualization of citation relationships (issue #36)
+
+### 🟢 Low Priority
+1. Add `find-dois` script run to CI for T2 articles
+2. T13 DOI completion — 7 technical reports/blog posts currently `% No DOI available`
+
+---
+
+**Prepared by**: Claude Opus 4.6  
+**Status**: All systems operational  
+**Next Action**: PR review by Codex