🔢 Johnny Decimal Master Index — PUMA Vault
Johnny Decimal principle: every file has a unique numeric address (AC.ID).
Overview
Areas: 10–90. Categories: 10–19 within each area. Sub-items: decimal. Rule: max 10 areas, max 10 categories per area, max 10 items per category (conceptually).
00 — Meta & System
| ID | Name | Link |
|---|---|---|
| 00.01 | Home Dashboard | 00 - Home |
| 00.02 | Recommended Plugins | Recommended-Plugins |
| 00.03 | Git/GitHub Setup | Git-GitHub-Setup |
| 00.04 | CSS Snippets | CSS-Snippets-Guide |
| 00.05 | Vault Guide | VAULT-GUIDE |
Templates (00.1x)
| ID | Template | Link |
|---|---|---|
| 00.10 | Fleeting Note | Template-Fleeting-Note |
| 00.11 | Literature Note (Paper) | Template-Literature-Note-Paper |
| 00.12 | Permanent Note | Template-Permanent-Note |
| 00.13 | Experiment Note | Template-Experiment-Note |
| 00.14 | Prompt Note | Template-Prompt-Note |
| 00.15 | Daily Review | Template-Daily-Review |
| 00.16 | Weekly Review | Template-Weekly-Review |
| 00.17 | Book Note | Template-Book-Note |
| 00.18 | Keshav Three-Pass Note | Template-Keshav-ThreePass |
| 00.19 | Sprint Board | Template-Sprint-Board |
10 — Inbox (GTD Capture)
| ID | Name | Link |
|---|---|---|
| 10.01 | README Inbox | README-Inbox |
| 10.02 | Quick Capture Log | Quick-Capture-Log |
| 10.10 | Fleeting Note Template | Template-Fleeting-Note |
20 — Literature (Sources)
Papers (20.1x)
| ID | Category | Link |
|---|---|---|
| 20.10 | Papers Index | README-Papers |
| 20.11 | LLM Agents General | README |
| 20.12 | Effort Estimation | README |
| 20.13 | PM + AI Convergence | README |
| 20.14 | Reproducibility in SE | README |
| 20.15 | Triage & Benchmarks | README |
| 20.16 | Key Papers (CoGEE, Angermeir, Flyvbjerg) | LN-KeyPapers-CoGEE-Angermeir-Flyvbjerg |
Other Sources (20.2x–20.7x)
| ID | Category | Link |
|---|---|---|
| 20.20 | Books | LN-Books-KeyReferences |
| 20.30 | Datasets (Jira SR + TAWOS) | LN-Datasets-JiraSR-TAWOS |
| 20.40 | Videos & Podcasts | LN-Videos-Repos-Community |
| 20.50 | Repositories & Code | README-Repos |
| 20.60 | Tools — Dev Stack | LN-Tools-Dev-Stack |
| 20.61 | Tools — Ollama + AI | LN-Tools-Ollama-ClaudeCode-OpenCode-BrowserOS |
| 20.62 | Tools — Research | LN-Tools-Research-Discovery |
| 20.70 | Web & Blog Resources | LN-Web-Resources |
30 — Permanent Knowledge (Zettelkasten)
Concepts (30.1x)
| ID | Permanent Note | Link |
|---|---|---|
| 30.10 | Concepts README | README-Concepts |
| 30.11 | CoT + Few-Shot Prompting | PN-CoT-FewShot-Prompting |
| 30.12 | Issue Triage + Story Points | PN-IssueTriage-StoryPoints |
| 30.13 | Agents + Reproducibility + Red Teaming | PN-KeyConcepts-Agents-Reproducibility-RedTeam |
| 30.14 | RAG + Embeddings + Vector DBs | PN-RAG-Embeddings-VectorDB |
| 30.15 | LLM Local vs Cloud Tradeoffs | PN-LLM-Local-vs-Cloud |
Methods (30.2x)
| ID | Permanent Note | Link |
|---|---|---|
| 30.20 | Methods README | README-Methods |
| 30.21 | DSR + SLR Methods | PN-DSR-SLR-Methods |
| 30.22 | Wilcoxon + FINER + Cornell + PRISMA | PN-Wilcoxon-FINER-Cornell-PRISMA |
Frameworks (30.3x)
| ID | Permanent Note | Link |
|---|---|---|
| 30.30 | Frameworks README | README-Frameworks-Results-Hypotheses |
| 30.31 | SDD Framework (SDD+OpenSpec+SpecKit+BMAD) | PN-SDD-Framework |
| 30.32 | RCOIF Framework | PN-RCOIF-Framework |
| 30.33 | EGI Framework | PN-EGI-Framework |
| 30.34 | AMI + DRCA + IIPR | PN-AMI-DRCA-IIPR-Frameworks |
| 30.35 | Keshav Three-Pass Method | PN-MIT-Student-Method |
| 30.36 | PARA + GTD + Zettelkasten Integration | PN-PARA-GTD-Zettelkasten |
40 — Projects (PARA Projects)
| ID | Name | Link |
|---|---|---|
| 40.10 | Ch.1 Introduction | PR-PUMA-Ch1-Introduction |
| 40.20 | Ch.2 Literature Review | PR-PUMA-Ch2-Ch3-Ch4-Ch5 |
| 40.30 | Ch.3 Methods | PR-PUMA-Ch3-Methods |
| 40.40 | Ch.4 Results | PR-PUMA-Ch4-Results |
| 40.50 | Ch.5 Discussion | PR-PUMA-Ch5-Discussion |
| 40.60 | Spec: Architecture v1 | SP-Architecture |
| 40.61 | Spec: Triage Agent | SP-Triage-Agent |
| 40.62 | Spec: Estimation Dataset | SP-Estimation-Dataset-Specs |
| 40.63 | Spec: Constitution | SP-PUMA-Constitution |
| 40.70 | Experiments: H1 + H2 | EX-Hypotheses-H1-H2 |
| 40.71 | Experiments: Stages Overview | EX-Stages-Overview |
| 40.80 | Sprint Board — PEC2 | Sprint-02 |
| 40.90 | BMAD Agent Roster | BMAD-Agent-Roster |
| 40.91 | BMAD PRD Document | BMAD-PRD-PUMA |
50 — Areas (PARA Areas)
| ID | Name | Link |
|---|---|---|
| 50.10 | AI Use Log | AI-Use-Log |
| 50.11 | PRISMA Log | PRISMA-Log |
| 50.12 | Keshav Three-Pass Library | Keshav-Reading-Log |
| 50.20 | Writing Progress Tracker | Writing-Progress-Tracker |
| 50.30 | Code Review Log | Code-Review-Log |
| 50.40 | Carbon Tracking Log | Carbon-Tracking-Log |
| 50.50 | Ethics Review Log | Ethics-Review-Log |
| 50.60 | Smart PMO Vision | Smart-PMO-Vision |
60 — Resources (PARA Resources)
| ID | Name | Link |
|---|---|---|
| 60.10 | PUMA Experiment Prompts | PT-PUMA-Experiment-Prompts |
| 60.11 | Claude RCOIF Research Prompt | PT-Claude-RCOIF-Research |
| 60.12 | All LLM Tool Prompts | PT-LLM-Tools-All-Prompts |
| 60.13 | Advanced Prompts (IIPR+Anchoring) | PT-Advanced-Prompts-IIPR-Anchoring-AgentOS |
| 60.14 | Research Discovery Prompts | PT-Research-Discovery-Prompts |
| 60.15 | Dev Tools Prompts | PT-DevTools-Prompts |
| 60.16 | BMAD Agent Prompts | PT-BMAD-Agent-Prompts |
| 60.20 | Workflow: Research + Experiment | WF-Research-Experiment-Routines |
| 60.21 | Workflow: SLR Pipeline | WF-SLR-Pipeline |
| 60.30 | Quality Checklists | CL-Quality-Checklists |
| 60.40 | Glossary Master | Glossary-Master |
| 60.50 | Bibliography APA7 | BIB-Master-APA7 |
| 60.60 | JD Master Index (this file) | JD-Master-Index |
70 — Archive (PARA Archive)
80 — MOCs (Maps of Content)
| ID | MOC | Link |
|---|---|---|
| 80.10 | PUMA Master Map | MOC-PUMA-Master |
| 80.11 | Research Pipeline | MOC-Research-Pipeline |
| 80.12 | Literature Review | MOC-Literature-Review |
| 80.13 | LLM Benchmarks + PM+AI | MOC-LLM-Benchmarks-PM-AI |
| 80.14 | Methods & Frameworks | MOC-Methods-Frameworks |
| 80.15 | Prompts Library | MOC-Prompts-Library |
| 80.16 | Tools Stack | MOC-Tools-Stack |
| 80.20 | Master Index (this JD) | JD-Master-Index |
90 — GTD System
| ID | Name | Link |
|---|---|---|
| 90.10 | Active Tasks | TASKS-Active |
| 90.20 | Projects Master List | PROJECTS-Master |
| 90.30 | Someday / Maybe | SOMEDAY-WAITING-PROJECTS |
| 90.40 | Waiting For | WAITING-Log |
| 90.50 | Daily Review Template | Daily-Review-Template |
| 90.51 | Weekly Review Template | Weekly-Review-Template |
| 90.60 | Sprint Board PEC2 | Sprint-02-Board |
JD Index version 2.0 — April 2026 — Updated for PEC2