🧠 AI Second Brain — an agent-operated PKM template for Obsidian

This repository is a template: clone it, open it in Obsidian, point your AI agent at it, and you have a working knowledge operating system — an ARA-structured vault plus a toolbelt of skills that turn raw bookmarks into strategic plans and tracked work. No personal areas or notes are included — you bring your own; the scaffolding and tooling are the product. The one deliberate exception is a single worked example — the standup-tools Area — shipped on purpose as an end-to-end demo of the Productize workflow (below).

✨ Why this exists

Most "second brain" setups rot: you capture endlessly and synthesize never. This template makes AI agents do the processing — curating captures, synthesizing drafts into plans, extracting tasks, and linting the knowledge graph — while you keep the judgment. It is agent-augmented, not agent-led.

• 🔁 A capture → curate → synthesize → act loop that prunes spent material as it goes (lite over large).
• 🧩 A toolbelt of skills (slash commands) that automate the boring parts.
• 🗂️ ARA structure (Areas / Resources / Archive) with a hard wall between Work, Personal, and Resources to stop context bleed.
• 🔗 Link-first: value lives in the [[wikilinks]], surfaced on a live dashboard.
• 🛡️ Security guardrails that stop agents from reading or exfiltrating your secrets (SSH keys, .env, cloud credentials, shell history).
• 🤝 Dual-agent peer review: one agent builds a tool, the other challenges and hardens it before it ships.

🔁 The Operating Loop

flowchart LR
    Inbox["00-inbox<br/>(raw bookmarks)"] --> Curate["curate-bookmarks"]
    Curate -->|extract signal| Draft["draft/<br/>(curated notes)"]
    Draft --> Synthesize["synthesize-drafts"]
    Synthesize -->|thematic synthesis| Plan["synthesis/<br/>(strategic plan)"]
    Plan --> Extract["plan-to-kanban"]
    Extract -->|dedupe + append| Kanban["todo-kanban.md<br/>(tasks)"]
    Kanban --> Execute["build / execute"]
    Execute --> Prune["delete spent<br/>intermediates"]

🗂️ Vault Structure (ARA)

🧰 The Toolbelt (Skills)

Run these as slash commands in Claude Code (or via the Skill tool); Codex invokes the same skills with $skill:

• /init-area — scaffold a new Area: challenge the idea, define goals/scope, create the hub note, Kanban board, and triage queue.
• /curate-bookmarks — turn inbox captures into per-Area "what can we steal" drafts; judge each link independently; log the source.
• /scout-idea — challenge an idea's value, then run a broad discovery sweep for tools/OSS/articles when you have no bookmarks yet.
• /synthesize-drafts — analyze an Area's drafts against each other with a scientific thematic matrix and produce one strategic plan.
• /plan-to-kanban — extract the plan's action items into the Area's Kanban board, deduplicated.
• /productize-new → /productize-report — a six-phase product toolkit: take an Area idea from intake → PRD → market/competitive/feasibility analyses → an honest Go/No-Go → build specs + roadmap → a capstone visual HTML report. Honest-by-design (thin evidence → low confidence; a weak case earns NO-GO/PIVOT).
• /vault-linter — read-only graph integrity check: broken [[wikilinks]], orphan notes, missing traceability.
• /audit-maintenance — headless cross-agent peer review that challenges and hardens newly built tools.
• /security-guardrails — install a portable deny-list plus a PreToolUse hook that blocks shell reads of secrets, in any project.

🏭 Productize — take an Area from idea to build specs

Once an Area's thinking has matured, the productize toolkit runs it through a six-phase pipeline — from a one-line spark to a Go/No-Go decision and, if it survives, build-ready specs:

productize-new (intake → PRD) → productize-analyze (16 analyses) → productize-decide (Go/No-Go) → productize-build (deliverables + roadmap) → productize-report (capstone HTML).

It is honest by design: thin evidence yields low confidence, and a weak case earns a NO-GO or PIVOT — not a rubber stamp.

See it run end-to-end on a real, deliberately ordinary idea — StandupZero ("auto-draft each developer's daily standup from their real activity"):

• 📖 Walkthrough: Productize showcase — the StandupZero run, narrated phase by phase.
• 📂 Every artifact: the standup-tools Area — PRD, 16 analyses, Go/No-Go, 13 deliverables + roadmap, plus the visual summary report.
• 📘 Reference: Productize documentation — how the phases, control plan, and analysis dependency map work.

🚀 Quickstart

1. Use this template (or clone the repo).
2. Open the vault/ folder in Obsidian and enable the bundled community plugins: Kanban, Tasks, Mermaid Tools, mdmenu.
3. Install Claude Code (and/or Codex) and open the repo as your project — the agent reads CLAUDE.md automatically (Codex reads it via the AGENTS.md symlink).
4. Create your first Area: /init-area.
5. Drop a link into vault/00-inbox/, then run /curate-bookmarks → /synthesize-drafts → /plan-to-kanban.

📚 Documentation

• Operating System doc — the full philosophy, the loop, peer review, and the complete skill reference.
• Productize toolkit — the six-phase idea → build-specs pipeline, with the StandupZero worked example.
• Vault conventions — frontmatter schema, tags, titles, link-before-close.
• CLAUDE.md — the master instruction set both agents follow (AGENTS.md is a symlink to it, so Codex reads the same rules).

🛡️ Security

AI agents operate inside the project directory only. The included security-guardrails skill wires up a permissions.deny list and a PreToolUse hook so agents can't read or exfiltrate credential stores, .env files, private keys, tokens, or shell history — even via a shell cat. Harden any repo with /security-guardrails.

🤝 Contributing

Issues and PRs welcome — especially new skills and workflow improvements. New tooling is expected to pass the dual-agent peer review described in the Operating System doc.

📄 License

CC BY-NC-SA 4.0 © 2026 Ibrahim Kobeissy. See LICENSE.

You may use, adapt, and share this template for non-commercial purposes with attribution, and must license any derivatives under the same terms. Commercial use requires separate permission.

The bundled Obsidian plugins under vault/.obsidian/plugins/ are third-party software and remain under their own original licenses (MIT/GPL) — see the carve-out in LICENSE.