PUMA Vault

📋 Tools — Documentation, Organisation & Productivity

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📋 Tools — Documentation, Organisation & Productivity

Overview

All tools for project documentation, knowledge management, diagrams, and academic writing.

Knowledge Management

Obsidian

  • URL: https://obsidian.md
  • Function: Markdown-based knowledge management with bidirectional links
  • Phase: F0 – continuous
  • PUMA use: PRIMARY knowledge management tool; this vault; PARA + GTD + Zettelkasten + Johnny Decimal integration; research documentation; sprint boards; literature notes (Keshav Three-Pass); permanent notes
  • Plugins: Dataview, Templater, Tasks, Kanban, Zotero Integration, Obsidian Git, Excalidraw, Pandoc, Calendar
  • Structure: See JD-Master-Index and VAULT-GUIDE

Notion + Notion AI

  • URL: https://www.notion.so
  • Function: Team knowledge base and task management with integrated AI
  • Phase: F0 – continuous
  • PUMA use: Centralised project information hub (complementary to Obsidian); meeting notes; task tracking during F3–F4 (when sprint velocity tracking needed beyond Obsidian Tasks plugin); AI for note synthesis
  • Justification: AI synthesis of notes without sending to external APIs (Notion AI processed within Notion’s infrastructure); useful for quick project status summaries

Academic Writing

Overleaf

  • URL: https://www.overleaf.com
  • Function: Collaborative online LaTeX editor
  • Phase: F5 (optional)
  • PUMA use (optional): Final TFG memoir typesetting in LaTeX if required; UOC template import; automatic reference formatting from Zotero BibTeX export
  • Note: UOC template in Word is the primary format; Overleaf is optional for higher typesetting quality

Grammarly

  • URL: https://www.grammarly.com
  • Function: Grammar and style corrector for English text
  • Phase: F3 – F5
  • PUMA use: Reviewing Abstract and English-language sections of the TFG memoir; all Grammarly suggestions reviewed and selectively applied by author
  • Note: Tool assists, author decides; no automatic acceptance of suggestions

Jenni AI

  • URL: https://jenni.ai
  • Function: AI-powered academic writing assistant
  • Phase: F3 – F5
  • PUMA use: Structuring formal academic sections with consistent style; maintaining academic register; citation format suggestions (verified manually)
  • Declaration: Used as structural assistant; all content written/verified by author (Marco Veritas)

Diagrams & Visualisation

Excalidraw

  • URL: https://excalidraw.com
  • Function: Collaborative whiteboard for architecture diagrams
  • Phase: F2 – F3
  • PUMA use: PUMA system architecture diagrams (7-layer SwarmPMO); LangGraph state machine visualisation; multi-agent communication flow diagrams for the TFG memoir
  • Obsidian integration: Excalidraw plugin for in-vault diagram editing → Excalidraw
  • Export format: SVG (vector) for memoir; PNG for Obsidian preview

draw.io (diagrams.net)

  • URL: https://www.drawio.com
  • Function: More formal diagram tool (UML, C4, flowcharts)
  • Phase: F2 – F3
  • PUMA use: Formal C4 architecture diagrams; sequence diagrams for agent interactions; class diagrams for data schemas
  • Justification: C4 model diagrams for Section 3 (Materials & Methods) architecture documentation

Mermaid (in GitHub)

  • URL: https://mermaid.js.org
  • Function: Diagrams-as-code in Markdown
  • Phase: F2 – F3
  • PUMA use: README.md sequence/flow diagrams in GitHub repository; versioned alongside code; renders automatically in GitHub Markdown
  • Example: LangGraph state transitions, experiment pipeline flow, agent communication patterns

Automation Tools

BrowserOS

  • URL: https://github.com/browseros-ai/BrowserOS
  • Function: Chromium-based browser with native AI agent capabilities for research and documentation automation
  • Phase: F0 – continuous
  • PUMA use:
    • Centralised organisation of research information (papers, decisions, tasks, drafts)
    • AI-assisted note synthesis and documentation organisation
    • Automated web research sessions for SLR paper discovery
    • Document management with AI integration
  • Justification: Natively integrates AI agents for document organisation and research workflows without requiring separate API calls; complements Obsidian for web-based research tasks

MOCs

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