PUMA Vault

📇 Master Index — Johnny Decimal

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📇 Master Index — Johnny Decimal

Every note in this vault has a unique Johnny Decimal address.

Overview

Format: AREA.CATEGORY-NoteKeyword (e.g., 30.31-ChainOfThought) This index is the authoritative list of all active notes.

00 — Meta

IDNoteTypeStatus
00.0000 - HomeHomeActive
00.01Template-Literature-Note-PaperTemplateActive
00.02Template-Permanent-NoteTemplateActive
00.03Template-Experiment-NoteTemplateActive
00.04Template-Prompt-NoteTemplateActive
00.05Template-Daily-ReviewTemplateActive
00.06Template-Weekly-ReviewTemplateActive
00.07Template-Book-NoteTemplateActive
00.08Template-Video-Tool-Repo-NotesTemplateActive
00.09Template-Video-Tool-Repo-NotesTemplateActive
00.10Template-Video-Tool-Repo-NotesTemplateActive
00.20Recommended-PluginsConfigActive
00.21CSS-Snippets-GuideConfigActive
00.30Dashboard-Research-ProgressDashboardActive
00.31Dashboard-Experiment-StatusDashboardActive

10 — Inbox

IDNoteTypeStatus
10.01Template-Fleeting-NoteTemplateActive
10.02Quick-Capture-LogLogActive
10.03README-InboxGuideActive

20 — Literature

20.1 Papers

IDNoteAuthorsYearPUMA Use
20.11LN-Datasets-JiraSR-TAWOS (TAWOS section)Tawosi et al.2022Dataset H2
20.12LN-KeyPapers-CoGEE-Angermeir-Flyvbjerg (CoGEE section)Tawosi et al.2024Baseline H2
20.13LN-Datasets-JiraSR-TAWOS (Jira SR section)Ortu et al.2015Dataset H1
20.14LN-Angermeir-2025-ReproducibilityAngermeir et al.2025Gap 1
20.15LN-Calikli-2025-RequestFormatsCalikli & Alhamed2025Gap 2
20.1620 - Literature/20.1 Papers/LN-Strubell2019-EnergyNLPStrubell et al.2019Gap 3
20.1720 - Literature/20.1 Papers/LN-Manzoor2025-AI-PMManzoor et al.2025Context
20.18PN-CoT-FewShot-Prompting (CoT section — Wei et al. 2022)Wei et al.2022Methods
20.19PN-CoT-FewShot-Prompting (Few-Shot section — Brown et al. 2020)Brown et al.2020Methods
20.20PN-DSR-SLR-Methods (DSR section — Hevner 2004)Hevner et al.2004DSR
20.21PN-DSR-SLR-Methods (DSR section — Peffers 2007)Peffers et al.2007DSR
20.22PN-Wilcoxon-FINER-Cornell-PRISMA (Wilcoxon — Wohlin 2012)Wohlin et al.2012Methods
20.23LN-Spichkova-2025-CognitiveAgentsSpichkova et al.2025Context
20.2420 - Literature/20.1 Papers/LN-Yonathan2025-LocalLLMsYonathan2025Context
20.2520 - Literature/20.1 Papers/LN-Berti2024-PM-LLM-BenchmarkBerti et al.2024Context
20.2620 - Literature/20.1 Papers/LN-Page2021-PRISMA2020Page et al.2021Methods
20.2720 - Literature/20.1 Papers/LN-Kitchenham2007-SLRKitchenham & Charters2007Methods

20.2 Books

IDNoteAuthorsYear
20.31LN-KeyPapers-CoGEE-Angermeir-Flyvbjerg (Flyvbjerg section)Flyvbjerg & Gardner2023
20.32LN-Books-KeyReferences (Allen 2001 — GTD)David Allen2001
20.33LN-Books-KeyReferences (Ahrens 2022 — Zettelkasten)Sönke Ahrens2022
20.34LN-Books-KeyReferences (Popper 1959 — Logic of Scientific Discovery)Karl Popper1959
20.35LN-Books-KeyReferences (Graeber 2018 — Bullshit Jobs)David Graeber2018

20.3 Datasets

IDNoteSizeTask
20.41LN-Datasets-JiraSR-TAWOS50K+ / 23K+Triage / Estimation

20.4 Videos & Podcasts

IDNoteChannelTopic
20.51LN-Videos-Repos-Community (Karpathy — LLM internals)Andrej KarpathyLLM internals
20.52LN-Videos-Repos-Community (Codina — SLR with AI)Lluis CodinaSLR with AI
20.53LN-Videos-Repos-Community (r/LocalLlama — benchmarks)r/LocalLlamaLocal models

20.5 Code Repositories

IDNoteRepoPurpose
20.61LN-Repos-ReferenceCode (SOLAR-group/TAWOS)SOLAR-group/TAWOSDataset
20.62LN-Repos-ReferenceCode (wassim249/fastapi-langgraph)wassim249/fastapi-langgraphReference arch
20.63LN-Repos-AgentFrameworks (vency-ai/agentic-scrum)vency-ai/agentic-scrumPM agents
20.64LN-Repos-ReferenceCode (groepl/Obsidian-Zettelkasten-Starter-Kit)groepl/Obsidian-Zettelkasten-Starter-KitVault base

20.6 Tools

IDNoteCategory
20.71LN-Tools-Ollama-ClaudeCode-OpenCode-BrowserOSInference + Coding
20.72LN-Tools-Research-DiscoveryResearch
20.73LN-Tools-Dev-StackDevelopment

30 — Permanent Notes (Zettelkasten)

31 Concepts

IDNoteMaturity
30.31-01PN-CoT-FewShot-Prompting🌿 Growing
30.31-02PN-IssueTriage-StoryPoints🌿 Growing
30.31-03PN-KeyConcepts-Agents-Reproducibility-RedTeam (LLM Agents section)🌱 Seedling
30.31-04PN-RAG-Embeddings-VectorDB🌱 Seedling
30.31-05PN-KeyConcepts-Agents-Reproducibility-RedTeam (Reproducibility section)🌿 Growing
30.31-06PN-KeyConcepts-Agents-Reproducibility-RedTeam (Uniqueness Trap section)🌿 Growing
30.31-07PN-LLM-Local-vs-Cloud🌿 Growing
30.31-08PN-MultiAgent-ArchitecturePatterns🌿 Growing
30.31-09PN-ReAct-AgentPattern🌿 Growing
30.31-10PN-Agentic-Science-Paradigm🌱 Seedling
30.31-11PN-PUMA-within-AgenticScience-Trajectory🌱 Seedling

32 Methods

IDNoteMaturity
30.32-01PN-DSR-SLR-Methods🌳 Evergreen
30.32-02PN-Wilcoxon-FINER-Cornell-PRISMA (Wilcoxon section)🌿 Growing
30.32-03PN-Wilcoxon-FINER-Cornell-PRISMA (FINER section)🌿 Growing
30.32-04PN-Wilcoxon-FINER-Cornell-PRISMA (Cornell section)🌿 Growing

33 Frameworks

IDNoteMaturity
30.33-01PN-RCOIF-Framework🌳 Evergreen
30.33-02PN-MIT-Student-Method🌳 Evergreen
30.33-03PN-EGI-Framework🌳 Evergreen
30.33-04PN-AMI-DRCA-IIPR-Frameworks🌳 Evergreen
30.33-05PN-SDD-Framework🌳 Evergreen
30.33-06PN-KeyConcepts-Agents-Reproducibility-RedTeam (Red Teaming section)🌿 Growing
30.33-07PN-KeyConcepts-Agents-Reproducibility-RedTeam (Agent OS section)🌿 Growing
30.33-08PN-Wilcoxon-FINER-Cornell-PRISMA (PRISMA-DFLLM section)🌿 Growing
30.33-09PN-Wilcoxon-FINER-Cornell-PRISMA (Contextual Anchoring section)🌱 Seedling

34 Results

IDNoteStatus
30.34-01RES-Results-Placeholders (Triage Stage 1 — pending)Pending
30.34-02RES-Results-Placeholders (Estimation Stage 2 — pending)Pending

35 Hypotheses

IDNoteStatus
30.35-01EX-Hypotheses-H1-H2Defined
30.35-02EX-Hypotheses-H1-H2 (Popper falsifiability — §H0 formulation)Evergreen

40 — Projects

IDNotePhaseStatus
40.41PR-PUMA-Ch1-IntroductionF0✅ Done
40.42PR-PUMA-Ch2-Ch3-Ch4-Ch5F0–F1🔄 Active
40.43PR-PUMA-Ch3-MethodsF1–F2🔄 Active
40.44PR-PUMA-Ch4-ResultsF4⏳ Pending
40.45PR-PUMA-Ch5-DiscussionF4–F5⏳ Pending
40.46SP-ArchitectureF1🔄 Active
40.47EX-Hypotheses-H1-H2F1✅ Defined

50 — Areas

IDNoteArea
50.51AI-Use-LogResearch
50.52PRISMA-LogResearch
50.53Writing-Progress-TrackerWriting
50.54Code-Review-LogDevelopment
50.55Carbon-Tracking-LogSustainability
50.56Ethics-Review-LogEthics

60 — Resources

IDNoteCategory
60.61PT-PUMA-Experiment-PromptsPrompts
60.62PT-Claude-RCOIF-ResearchPrompts
60.63PT-Research-Discovery-PromptsPrompts
60.64PT-DevTools-PromptsPrompts
60.65WF-SLR-PipelineWorkflows
60.66WF-Research-Experiment-RoutinesWorkflows
60.67WF-MIT-AILab-Reading-WorkflowWorkflows
60.68WF-Research-Experiment-RoutinesWorkflows
60.69CL-Quality-ChecklistsChecklists
60.70Glossary-MasterReference
60.71BIB-Master-APA7Bibliography

80 — MOC

IDNote
80.80MOC-PUMA-Master
80.81MOC-Research-Pipeline
80.82MOC-Literature-Review
80.83MOC-LLM-Benchmarks-PM-AI
80.84MOC-AI-Knowledge-Generation
80.85MOC-Prompts-Library
80.86MOC-Methods-Frameworks
80.87MOC-Tools-Stack
80.88Master-Index

90 — GTD

IDNote
90.91TASKS-Active
90.92PROJECTS-Master
90.93SOMEDAY-WAITING-PROJECTS
90.94WAITING-Log
90.95Daily-Review-Template
90.96Weekly-Review-Template

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