obsidian-second-brain

Crew: one logbook for all your agents

Crew works without Obsidian. Claude Code, Codex, Cursor, and Grok Bot share job records in any plain folder. Each agent sees what the others finished and can leave a lesson for review.

• Grok Bot joins the same team through its existing runner.
• A lesson becomes a rule only when a human runs keep.
• Crew runs no background loop.

curl -fsSL https://raw.githubusercontent.com/eugeniughelbur/obsidian-second-brain/main/scripts/quick-install.sh | bash

Restart Claude Code, then type /crew setup. Pick ~/crew or wiki/team/ inside your Obsidian vault. Codex users run /hooks once to trust Crew's hooks. Setup prints a Grok Bot profile block to paste.

18:40 | codex | brand | Astra pass, 0 errors

Setup, exact commands, and limits. Python 3.10 or later; no extra packages for Crew. Shared agent memory isn't new. What Crew adds is the three parts above.

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The Problem

You use Claude every day. Every session starts from scratch. You re-explain everything. The conversation ends. Everything disappears. Claude Code has no persistent memory across sessions - and neither does Grok Bot, Codex, Gemini, or any of the others.

You take notes in Obsidian. Hundreds of files. They just sit there. You make the same decision twice because you forgot you made it six months ago. Ideas rot in daily notes. Nobody connects the dots.

Two powerful tools. Completely disconnected. You already have the long-term memory. The thing doing the thinking cannot reach it.

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Who builds this

I'm Eugeniu Ghelbur, an AI automation engineer. I built this for my own vault, and I still run my work on it every day. I review and merge every change myself, and close to 50 people have shipped fixes so far (see who).

I write up what I learn twice a week on The AI Operator, and post shorter notes on X and LinkedIn.

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How this extends Karpathy's LLM Wiki

Karpathy's pattern is brilliant. Drop sources, LLM creates wiki pages, ask questions. This skill takes it further:

	Karpathy's LLM Wiki	obsidian-second-brain
New sources	Append new pages, cross-reference	Rewrite existing pages. People get updated, claims revised, stale facts replaced.
Contradictions	Flagged, you resolve manually	/obsidian-reconcile resolves them automatically
Patterns	Surface when you ask	/obsidian-synthesize finds unnamed patterns and writes synthesis pages on its own
When it runs	On demand, when you prompt	4 scheduled agents: morning brief, nightly consolidation, weekly review, vault-health check
Note format	Human-readable wiki pages	AI-first: ## For future agent preamble + frontmatter for LLM retrieval, not human review

If Karpathy's wiki is a knowledge base you maintain with an LLM, this is a knowledge base that maintains itself.

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What Happens When You Install This

After a meeting: /obsidian-save Claude pulls out every decision, person, task, and idea and saves each one to the right note. You do nothing.

You recorded a voice memo: /obsidian-ingest meeting.m4a Claude transcribes it with a local Whisper install, attributes speakers where the transcript makes them identifiable, extracts every promise and action item, and distributes across entity pages, task boards, and the daily note.

You screenshot a whiteboard: /obsidian-ingest photo.png Claude reads the image, extracts text and structure, creates concept notes, links to related projects. A photo becomes knowledge.

You have a finished text document: /obsidian-ingest report.docx Word (.docx, .doc) and OpenDocument (.odt) files uploaded or copied into the vault follow the same local-source rules as PDFs and Markdown. The helper converts a private copy to a temporary PDF, then ingestion uses the existing PDF path. Text and figures use that path; comments and revision markup are excluded. The original stays unchanged and remains the source under the existing provenance rules. Requires Python 3.10+ and LibreOffice 26.2+, installed separately. Run python scripts/document_to_pdf.py "path/to/report.docx"; it prints the PDF path. Put soffice on PATH or add --soffice with its executable path (Windows: C:/Program Files/LibreOffice/program/soffice.com; macOS: /Applications/LibreOffice.app/Contents/MacOS/soffice). Remove the generated PDF and its temporary parent folder after capture. No additional Python packages are needed. See the ingest command. Presentation and spreadsheet formats remain outside scope.

You find a great video: /obsidian-ingest https://youtube.com/... Claude doesn't summarize into one note. It REWRITES your existing pages. People get updated. Contradictions get resolved. Patterns trigger new synthesis pages. One URL in. The vault is smarter.

Before a big decision: /obsidian-challenge Claude searches your vault for past failures and reversed decisions on the same topic. Pushes back with your own words. Your vault holds you accountable.

You want to see the big picture: /obsidian-visualize Claude generates a visual canvas of your entire vault. Hub nodes centered, color-coded by type, orphans highlighted. Open it in Obsidian and see the shape of your knowledge.

You go to sleep: The nightly agent runs 5 phases: closes the day, reconciles contradictions, synthesizes cross-source patterns, heals orphan notes, and rebuilds the index. You wake up to a smarter vault.

You start a new day: /obsidian-daily Claude pulls your calendar events, overdue tasks, and overnight changes into today's note. Your morning starts informed.

Someone shares an X post: /x-read https://x.com/... Grok with live X access fetches the post, the thread, and the replies. Returns verbatim text + TL;DR + key claims + reply sentiment + voices to watch. No more screenshots.

You're planning today's content: /x-pulse "AI automation" Grok scans X for what's trending in your topic right now. Returns 3-5 emerging themes (with rep posts + key voices), gaps nobody is filling, hook formats that are working, and 3 specific post ideas you could write today.

You need real research: /research "AI memory tools" Perplexity Sonar Pro pulls a deep dossier with citations: summary, key facts (every claim with a recency marker and source domain), timeline, key players, contrarian views, recommended further reading, open questions. Saved to your vault, auto-opens in Obsidian.

You want vault-first deep research: /research-deep "AI memory tools" Scans your vault for what you already know. Identifies gaps. Spawns 3-5 targeted searches via Perplexity (web) and Grok (X discourse). Synthesizes a delta report: what's new, what's confirmed, contradictions to resolve, recommended vault updates. Vault baseline doesn't get re-researched. Only gaps get filled.

You hit a great YouTube video: /youtube https://youtu.be/... Free transcript via youtube-transcript-api. Optional metadata + top comments via YouTube Data API v3. Gemini (free tier, Grok fallback) summarizes into TL;DR, Key Points, Notable Quotes (verbatim), Themes, Comment Sentiment, and Worth Following Up On. Saved as an AI-first note in your vault. Add --visual to also watch it: scene-change frame extraction (ffmpeg) that Claude reads with its own vision to capture on-screen text, code, diagrams, and demos the transcript misses.

You never open Obsidian. Everything happens through Claude.

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Before & After

	Without this skill	With this skill
Saving decisions	Copy-paste or lose them	Auto-saved to the right project note
Daily notes	Write it yourself, forget half the time	Created automatically
Finding patterns	Re-read dozens of notes	/obsidian-emerge finds them for you
Challenging yourself	Nobody pushes back	/obsidian-challenge uses your own history against you
Session continuity	Re-explain every time	/obsidian-world loads full context in 10 seconds
Ingesting content	Read it, forget it	/obsidian-ingest rewrites 5-15 vault pages from 1 source (URLs, PDFs, Word/OpenDocument text files, audio, screenshots)
Contradictions	You don't know they exist	/obsidian-reconcile resolves them automatically
Synthesis	You connect dots manually	/obsidian-synthesize finds patterns across sources on its own
Sharing vault data	Only Claude can read it	/obsidian-export gives any AI tool a clean snapshot
Facts change over time	Old info gets overwritten	Bi-temporal facts track when it was true AND when the vault learned it
Starting a new session	Re-explain who you are	CRITICAL_FACTS.md loads your identity in ~120 tokens
Reading an X thread	Open X, scroll, screenshot, paste	/x-read [url] returns post + thread + sentiment + voices
Knowing what to post	Guess what's trending	/x-pulse scans X and returns hot themes + gaps + hooks + post ideas
Web research	Open 12 tabs, copy quotes manually	/research [topic] returns a sourced dossier with recency markers
Researching what you already know	Re-research from scratch	/research-deep scans vault first, fills only the gaps, flags contradictions
YouTube videos	Watch passively, forget	/youtube [url] transcript + summary + quotes saved to vault
Vault notes for future agent	Notes for human reading	AI-first rule: every note has "For future agent" preamble + recency markers + citations

More from the author

The product is above. This is where it came from and where it goes next.

Follow along

Two posts a week on AI second-brain systems, vault patterns, and what works in practice.

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---

How It Works

  +------------------------------------------+
  |                                          |
  |   LAYER 1: Operations (32 commands)      |
  |   Claude remembers everything            |
  |                                          |
  +------------------------------------------+
  |                                          |
  |   LAYER 2: Thinking Tools (9 commands)   |
  |   Claude thinks with you                 |
  |                                          |
  +------------------------------------------+
  |                                          |
  |   LAYER 3: Context Engine (1 command)    |
  |   Claude knows who you are               |
  |                                          |
  +------------------------------------------+
  |                                          |
  |   LAYER 4: Research Toolkit (7 commands) |
  |   Claude pulls knowledge in              |
  |                                          |
  +------------------------------------------+
  |                                          |
  |   ALWAYS ON                              |
  |   Background agent + 4 scheduled agents  |
  |   Auto-synthesis + save reminders        |
  |                                          |
  +------------------------------------------+

49 commands total. The calendar command (/obsidian-calendar) is Claude Code only (needs the Google Calendar MCP), so the Codex / Gemini / OpenCode / Hermes / Pi / Agent Skills builds ship 48.

Layer 1 saves, organizes, ingests, reconciles, exports, schedules your calendar, and maintains your vault. Layer 2 challenges your ideas, surfaces hidden patterns, bridges unrelated domains, and graduates ideas into projects. Layer 3 loads your identity and current state so every session picks up where the last one ended. Layer 4 pulls live external knowledge into the vault: X posts, X trends, web research with citations (key-less by default), YouTube and podcast transcripts. Vault-first synthesis knows what you already know. Always On keeps the vault alive without you lifting a finger.

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49 Commands

Operations -- Claude remembers

Command	What it does
/obsidian-save	Saves everything from the conversation -- decisions, tasks, people, ideas
/obsidian-ingest	Ingest a URL, file, or resumable folder batch (text, PDFs, .docx/.doc/.odt via LibreOffice, audio, images). The vault REWRITES itself. 5-15 pages touched per source.
/obsidian-synthesize	Auto-finds patterns across sources and writes synthesis pages
/obsidian-reconcile	Finds contradictions and resolves them. The vault maintains its own truth.
/obsidian-checkin	Asks you whether old people and project notes still hold. Shows what each says, re-asks until you answer, saves the news.
/obsidian-export	Clean JSON/markdown snapshot any AI tool can read
/obsidian-daily	Creates or updates today's daily note
/obsidian-calendar <mode>	One calendar command, four modes: agenda (read a snapshot), reconcile (flag commitments not yet scheduled), meeting (event to note), schedule (create/move an event from a task or standalone)
/obsidian-recurring	Tracks a recurring obligation with a cadence and a computed next-due date
/obsidian-log	Logs a work session, links it everywhere
/obsidian-task	Adds task to the right board with priority and due date
/obsidian-person	Creates or updates a person note
/obsidian-capture	Zero-friction idea capture
/obsidian-catchup	Process captures dumped from the Telegram bot (voice/text/image/PDF/link) into the vault
/obsidian-find	Smart search with context
/obsidian-recap	Summary of a day, week, or month
/obsidian-review	Structured weekly or monthly review
/obsidian-board	Kanban board view and updates
/obsidian-board-hygiene	Bulk-triage a board -- surface stale/overdue items, then archive / reschedule / mark-Done in one pass
/obsidian-project	Project note with board and daily links
/obsidian-projects	Live project status from git + local docs -- infers all context from vault notes, no config required
/obsidian-health	Vault audit -- contradictions, gaps, stale claims, orphans, freshness violations (the freshness policy: every fact timeless, dated, or a pointer), typed-edge lint (unknown types, dangling targets, contradiction cycles in the relations: graph), and a tag taxonomy audit (opt-in via _meta/taxonomy.md)
/obsidian-merge	Merge two near-duplicate notes from /obsidian-health into one -- dry run by default, frontmatter union, retired note becomes a redirect (never deleted)
/obsidian-reindex	Refreshes the incremental semantic index and reports coverage before and after, with clear embedding-backend failures
/obsidian-retrieval-eval	Measures vault search quality -- recall@k + MRR on natural-language questions, with the concrete failures and ranked fixes
/obsidian-decide [--formal]	Logs decisions to the right project notes; --formal writes a full ADR record (the vault knows why it's structured this way)
/obsidian-visualize	Generates a visual canvas map of your second brain
/obsidian-learn	Reviews vault learnings, prunes stale ones, surfaces patterns to promote into rules
/obsidian-init	Generates _CLAUDE.md, index.md, log.md
/obsidian-architect	Scans a codebase and writes maintained architecture notes (overview, modules, decisions) into the vault; re-run to refresh
/crew setup	Shared job log and lessons with a human keep decision; works without Obsidian
/create-command	Interview flow that scaffolds a new command into commands/<name>.md, no markdown editing

Thinking -- Claude thinks with you

Command	What it does
/obsidian-brainstorm [topic]	Multi-turn Socratic interview - one question per turn until the idea converges, then a design note with named alternatives
/obsidian-challenge	Your vault argues against your idea using your own history
/obsidian-panel	Convenes a panel of distinct perspectives on a decision, one verdict each + synthesis
/obsidian-emerge	Surfaces patterns from 30 days of notes you never named
/obsidian-connect [A] [B]	Bridges two unrelated domains to spark new ideas
/vault-deep-synthesis [topic]	Cross-references every note on a topic: agreements, contradictions, stale claims, gaps
/obsidian-distill [note or source]	Condenses a long note/source into key claims, each tagged with provenance back to the exact source block
/idea-discovery	Ranks 3-5 next-direction candidates from ideas, open questions, and orphan research
/obsidian-graduate	Turns an idea fragment into a full project with tasks

Context -- Claude knows you

Command	What it does
/obsidian-world	Loads identity + state with progressive token budgets (L0-L3)

Research -- Claude pulls knowledge in

Powered by xAI Grok (live X access) + Perplexity Sonar (web research) + YouTube. Findings save to Research/ as AI-first notes (preamble, frontmatter, recency markers, sources verbatim).

Command	What it does
/x-read [url]	Deep-read an X post: verbatim post + thread + TL;DR + claims + reply sentiment + voices
/x-pulse [topic]	Scan X for what's trending: themes, voices, hooks, post ideas
/research [topic]	Web research with citations: full dossier with recency markers and open questions. Uses Perplexity when keyed, free key-less sources (Wikipedia, HackerNews, arXiv, Reddit, and more) otherwise
/research-deep [topic]	Vault-first synthesis (open web): scans your vault, finds gaps, fills them via Perplexity + Grok (or free key-less sources when unkeyed), propagates updates across people/projects/ideas
/notebooklm [topic]	Vault-grounded synthesis via Gemini File Search. Uploads top 12 vault notes, returns a grounded answer with citations. No browser, one HTTP call. Pairs with /research-deep for dual-track research.
/youtube [url] [--visual]	Extract transcript + metadata + top comments → AI-first summary. --visual adds scene-change frame extraction Claude reads with its own vision
/podcast [url]	Apple Podcasts or RSS → transcript (RSS tag / Whisper / show-notes) + AI-first summary

Setup: copy .env.example to ~/.config/obsidian-second-brain/.env, add your keys (xAI, Perplexity, YouTube optional, OpenAI optional for podcast Whisper). Run install.sh and answer "y" to the research prompt to do this automatically.

No keys? /research and /research-deep still work. With no PERPLEXITY_API_KEY set they automatically fall back to free, key-less sources (Wikipedia, HackerNews, arXiv, Reddit, Lobsters, dev.to, OpenAlex, Semantic Scholar, CrossRef, DuckDuckGo - plus Tavily/Brave when keyed and Keenable when RESEARCH_KEENABLE=1) and Claude synthesizes the dossier. Pass --free to force it even when keyed, or --academic to restrict to scholarly sources. The other research commands (/x-read, /x-pulse, /notebooklm, /youtube) still need their respective keys.

Optional Keenable source, off by default. Set RESEARCH_KEENABLE=1 to add Keenable web search to the free pool; unset, it never runs, and KEENABLE_API_KEY alone does not switch it on. Keenable runs this source, and your query text is sent to Keenable (api.keenable.ai). The anonymous limit is 1,000 requests an hour and 10 a second per IP; an optional KEENABLE_API_KEY lifts it.

/obsidian-challenge

You: "I want to rewrite the API in Rust."

Claude finds your 2025 post-mortem where the Rust rewrite failed. Finds your decision log committing to TypeScript for 2 years. Says: "Your own notes say this failed. Still want to proceed?"

---

/obsidian-emerge

Claude scans 30 daily notes. You mentioned "onboarding friction" in 4 unrelated projects.

"Onboarding is your bottleneck across projects. You never named it."

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/obsidian-connect "distributed systems" "cooking"

Traces both clusters in your link graph. Finds shared concepts: preparation and load distribution. Generates 3 actionable ideas at the intersection.

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/obsidian-graduate

An idea from 3 weeks ago. Claude reads it, finds related projects and people, generates a full spec with goals, phases, tasks, and board entries. The idea gets tagged graduated.

/obsidian-ingest https://youtube.com/watch?v=example

1. Saves original to raw/videos/ (immutable)
2. REWRITES entity pages with new context
3. REWRITES concept pages if the source adds depth or contradicts them
4. Creates synthesis pages when patterns emerge
5. Resolves contradictions and documents why
6. Updates index.md, log.md, daily note

One URL in. The vault rewrites itself.

/x-read https://x.com/garrytan/status/2048121438914154664

Grok with live X access fetches the post and replies. You get verbatim text, TL;DR, key claims, reply sentiment (~70% positive, 20% skeptical, 10% off-topic), notable counter-arguments with the @ handles of who said them, and "voices to watch" (the replies that added real signal). ~$0.05/call.

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/x-pulse "AI automation"

WHAT'S HOT (last 24-72h)
  1. Agentic AI vs Basic Automation — voices: @NVIDIAAP, @woisau1
  2. Self-Improving Sovereign Agents — voices: @tom_doerr, @AIDailyGems
  3. Control Layers & Execution Gaps — voices: @ZIQING_JP

WHAT'S UNDEREXPLORED
  - ROI numbers for non-developer small business users
  - Integration of digital agents with physical robotics

HOOKS THAT ARE WORKING
  - "Automation executes. Autonomy reasons." — @NVIDIAAP

POST IDEAS FOR YOU TODAY
  1. Thread: "I gave an open-source agent its own GitHub repo and watched it self-improve"
  2. Single: "Automation executes. Autonomy reasons. Here's the control layer..."

What you'd spend 2 hours scrolling X to find. Returned in 30 seconds for ~$0.13.

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/research "AI memory tools"

Returns a structured dossier: Summary, Key Facts (each with (as of YYYY-MM, source.com)), Timeline, Key Players, Contrarian Views, Recommended Further Reading, Open Questions, full citations. Saved to Research/Web/ as an AI-first note. ~$0.05/call.

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/research-deep "AI memory tools"

Phase 1: Vault scan
  Found 8 relevant notes (e.g. Knowledge/2026-02-15 - Mem0 vs Letta.md)

Phase 2: Gap analysis (Perplexity sonar-pro)
  Identified 5 targeted queries to fill what vault is silent or stale on

Phase 3: Targeted research
  [web] Anthropic Claude memory tool 2026 features
  [web] Mem0 Series A reactions and concerns
  [x]   developer reactions to Letta vs Mem0
  ...

Phase 4: Synthesis (sonar-reasoning-pro)
  → What's New Since Vault Baseline
  → What's Confirmed
  → Contradictions / Updates Needed (with [[wikilinks]] to specific vault files)
  → Synthesis bullets
  → Recommended Vault Updates (instructions for /obsidian-save)
  → Open Questions

Vault-first means it doesn't waste tokens re-researching what you already knew. ~$0.40/call.

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/notebooklm "AI-first vault rule" - vault-grounded, no browser

Scans the vault, uploads the top 12 most relevant notes to a Gemini File Search store, asks Gemini 2.5 Flash to synthesize against THOSE sources only with citations, writes the synthesis to Research/NotebookLM/ as an AI-first note, deletes the store.

Vault baseline: 12 notes
Model: gemini-2.5-flash
Uploading 12 notes... done
Asking Gemini, grounded against the uploaded sources...

=== SAVED ===
Research/NotebookLM/2026-05-15 - ai-first-vault-rule.md

Pair with /research-deep on the same topic. Open-web view + vault-grounded view rarely contradict. Where they do, that's where you have a take worth posting. ~$0.004/call on free-tier Flash, ~$0.06 on paid Pro.

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/youtube https://youtu.be/... (add --visual to watch, not just read)

Free transcript via youtube-transcript-api + optional metadata + comments via YouTube Data API v3 (free tier). Gemini (gemini-2.5-flash, free tier) summarizes into TL;DR, Key Points, Notable Quotes (verbatim), Themes, Comment Sentiment, and Worth Following Up On - Grok is the automatic fallback (~$0.04) when no Gemini key is set. Frontmatter includes view count, channel, published date, like count for Dataview queries.

--visual downloads the video (yt-dlp, <=720p) and extracts one frame per scene change (ffmpeg scene detection, not a fixed timer), so on-screen text, code, diagrams, slides, UI, and b-roll are captured. Claude reads the frames with its own vision (no extra API call) and writes a timestamp-keyed ## Visual notes section; hero frames are embedded in the note. Requires yt-dlp + ffmpeg on PATH; skips gracefully if missing. --max-frames N caps frames read (default 24). Pipeline ported from claude-watch / claude-video (MIT).

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/podcast https://podcasts.apple.com/... (or paste an RSS feed URL)

Resolves Apple Podcasts URLs to RSS via the free iTunes Lookup API. Picks the best transcript source available: <podcast:transcript> tag in the RSS feed (free, high fidelity) → Whisper API if OPENAI_API_KEY is set (~$0.006/min) → show-notes fallback. Grok summarizes into TL;DR, Key Points, Notable Quotes, Themes, Guests & People Mentioned, and Worth Following Up On. ~$0.04 for the Grok call (plus Whisper if used). Spotify URLs aren't supported (DRM).

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Auto-open after every save. Obsidian pops open at the new note. Disable with RESEARCH_AUTOOPEN=0 if you're running batch saves.

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The Vault is Alive

Traditional vaults are filing cabinets. You put things in. They sit there.

This vault rewrites itself with every input:

• Ingest a source -- existing pages get rewritten, contradictions resolved, patterns synthesized
• Save a conversation -- entities, concepts, and decisions distribute across the vault
• Ask a question -- the Two-Output Rule means every answer also updates pages
• A fact changes -- bi-temporal facts track when it was true AND when the vault learned it. "You believed X on Tuesday. After ingesting Y on Wednesday, you shifted to Z." Full audit trail.
• Do nothing -- background agent and scheduled agents maintain it while you sleep
• Wait a week -- auto-synthesis finds cross-source patterns and writes connection pages

The vault after a week is fundamentally different from the vault you started with.

The maintenance layer has a name: OKM (Open Knowledge Metabolism). Storage is the easy half; keeping stored knowledge true is the hard half, and it is where this project spends its effort. OKM is the open spec behind that: every stored fact must be timeless, dated, or a pointer. Slow-changing knowledge (how things work, decisions, ownership) is stored; fast-changing facts (counts, statuses, balances) are linked to where they live with an as of stamp, never copied in to rot. The rule is a one-page spec (references/freshness-policy.md), enforced by a linter (scripts/freshness_lint.py) that /obsidian-health runs. It is the companion to OKF (Google's Open Knowledge Format), and the division is sharper than format-versus-freshness: OKF v0.2 added fields for recording that something went stale (status, stale_after, verified), but a field cannot stop a note claiming "the pipeline has 13 deals" with no stamp on it. OKM is the rule about what may be stored bare at all, and a linter that fails the build when it is not. One spec, one reference linter, no second implementation yet. It is storage-agnostic: any folder of markdown an AI maintains, not just Obsidian vaults.

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Choose Your Preset

Pick your role at bootstrap. Each preset creates tailored folder structures, templates, and kanban boards.

Preset	Who it's for	Kanban style
executive	Founders, operators, managers	OKRs / Quarterly / Weekly
builder	Developers, engineers, architects	Backlog / Sprint / Done
creator	Writers, YouTubers, marketers	Ideas / Drafts / Published
researcher	Academics, analysts, deep-divers	Reading / Processing / Synthesized

uv run python scripts/bootstrap_vault.py --path ~/my-vault --name "Your Name" --preset builder

No preset? You get a general-purpose vault that works for everyone.

Every preset builds the Obsidian-style layout (Daily/, People/, Projects/, ...). Add --style wiki for the wiki-style layout described under Vault Architecture:

uv run python scripts/bootstrap_vault.py --path ~/my-vault --name "Your Name" --preset builder --style wiki

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Background Agent & Scheduled Agents

Background: fires after every context compaction. You keep working. The vault updates itself.

PostCompact -> obsidian-bg-agent.sh -> claude -p (headless) -> vault updated

What arming it costs. The headless run uses --dangerously-skip-permissions, because nobody is there to approve each write. That is why the agent ships inert and stays opt-in. Its tool surface is restricted with --tools "Read,Write,Edit,Glob,Grep" (the flag that removes every other built-in tool, not just pre-approves these) and no MCP servers are loaded, so it cannot run shell commands or reach the network, and it only adds and updates - it never deletes or merges. If that trade is not one you want, leave it off; every other command works without it.

Scheduled:

Agent	When	What
morning	8 AM	Daily note + overdue tasks
nightly	10 PM	Sleeptime consolidation: close day + reconcile + synthesize + heal orphans
weekly	Fridays 6 PM	Weekly review
health	Sundays 9 PM	Vault health audit

Save reminders: Claude nudges you to /obsidian-save after 10+ exchanges or when you say "done" or "thanks". No lost conversations.

Bounded recall (opt-in): on every prompt, a UserPromptSubmit hook injects a small brief of the most relevant vault notes - max 4 notes, ~900 chars - or nothing at all when confidence is low (abstention beats noise). Read-only, fail-closed, and every inject/abstain decision is logged to <vault>/.claude-runs/ for audit. Ships inert; arm it with OBSIDIAN_RECALL_ENABLED=1 per hooks/recall.hook.example.json.

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Vault Architecture

Starting with personal notes? /obsidian-init offers an optional First-Brain wiki-style variant for an existing, evolving collection of human notes. Human notes live in the First-Brain/ folder, immutable ingestion captures in raw/, and AI-maintained knowledge in wiki/. Initialization ensures the First-Brain/ source folder exists and configures ownership and routing; it does not move or ingest notes. Then use /obsidian-ingest on an individual First Brain file or the collection. Original notes stay in place under instruction-based protection, not a filesystem sandbox. See the initialization command for the full procedure.

Importing a collection? /obsidian-ingest Sources/ --preview discovers eligible text files, PDFs, audio, and images without reading source bodies or writing progress. /obsidian-ingest Sources/ --batch-size 10 processes up to ten sources sequentially through the existing ingestion workflow. Repeat the same command for the next batch or after an interrupted session has stopped; completed unchanged sources are skipped, and unfinished sources reuse their raw captures. Sensitive-content rules and rewrite approvals still apply. Required pending or declined approvals never count as completion.

Progress uses one hidden completion comment per processed source version in existing Logs/YYYY-MM-DD.md files, or legacy log.md; there is no separate state file or additional readable status line. The comment contains the source path, byte hash, raw reference, and timestamp. Each source finishes its catalog, daily-note, and normal log updates before the comment is written. Unfinished work has no completion comment and is retried on the next run; errors and pending approvals appear in the normal report. Removing completion history requires reprocessing, with raw deduplication retained. Run only one folder ingestion per vault at a time; this minimal helper does not track active sessions, enforce locking, or validate semantic extraction quality. See the ingestion procedure for supported extensions, provenance hashes, custom routing, and recovery. First Brain warm start is simply /obsidian-ingest First-Brain/; other layouts and source collections use the same workflow. Binary originals remain untouched; captures retain existing transcripts, PDF extracts, or image descriptions rather than archive binaries.

Two layouts are supported. scripts/bootstrap_vault.py builds the Obsidian-style layout by default: Daily/, People/, Projects/ and the preset's topic folders such as Goals/ and Mentions/, as laid out in references/vault-schema.md. Pass --style wiki for the wiki-style layout below. A preset folder the wiki layout renames moves to that name (People/ to wiki/entities/, Ideas/ and Knowledge/ to wiki/concepts/); one it does not rename keeps its own name under wiki/ (Goals/ to wiki/goals/, Sources/ to wiki/sources/), so a preset builds the same vault in either layout.

Wiki-style -- LLM-first

Claude is the reader and writer. The vault is a database.

vault/
+-- _CLAUDE.md          # Operating manual
+-- index.md            # Page catalog (Claude reads FIRST)
+-- log.md              # Activity timeline
+-- SOUL.md             # Your identity
+-- CRITICAL_FACTS.md   # ~120 tokens, always loaded (timezone, manager, location)
+-- raw/                # IMMUTABLE source material
+-- wiki/               # Claude's workspace
|   +-- entities/       # People, companies, tools
|   +-- concepts/       # Ideas, frameworks, synthesis
|   +-- projects/       # Project notes
|   +-- daily/          # Daily notes
|   +-- logs/           # Work session logs
|   +-- reviews/        # Weekly/monthly reviews
|   +-- tasks/          # Task notes
|   +-- decisions/      # ADRs
+-- boards/             # Kanban boards
+-- templates/          # Note templates

---

Install

One codebase, eight builds. Pick yours below. The vault behavior is identical across all of them; only the install path and the dispatcher file (CLAUDE.md / AGENTS.md / GEMINI.md / .agents/skills/ / .pi/ / workflow SKILL.md) differ.

Rather than ask you to take that on faith, here is what each build currently passes:

Build	Emits a real tree	Script paths resolved	Docs reachable	Toolkit runnable
Agent Skills	pass	pass	pass	pass
Claude Code	pass	pass	pass	pass
Codex CLI	pass	pass	pass	pass
Gemini CLI	pass	pass	pass	pass
Grok Bot	pass	pass	pass	pass
Hermes	pass	pass	pass	pass
OpenCode	pass	pass	pass	pass
Pi	pass	pass	pass	pass

Generated by scripts/conformance_report.py, verified in CI on every push. Each build is compiled from the same source tree, then checked for a non-empty output, a resolved script root, reference paths that actually exist in that build, and a Python project shipped beside the scripts. A red cell here is a real red cell, not a missing test.

Prerequisites: Claude Code (or one of the other six platforms below), git, and uv for the Python helpers (health check, research toolkit, bootstrap). jq is required for the classic script install - scripts/setup.sh uses it to edit ~/.claude/settings.json safely and exits if it is missing. Not needed on the plugin path. Optional: Ollama for local semantic search, openai-whisper (installed on first audio ingest, pulls in PyTorch). No API keys needed for the core vault commands.

Crew only (no vault)

Want the shared logbook without Obsidian? Run the quick install above, restart Claude Code, and type /crew setup. Pick a plain folder such as ~/crew. Or run the helper directly:

python3 ~/.claude/skills/obsidian-second-brain/scripts/crew.py --dir ~/crew setup

Codex users then run /hooks once to trust the hooks. Restart Cursor after setup. Full guide: references/crew.md.

Claude Code (default)

Native plugin install (recommended). Inside any Claude Code session:

/plugin marketplace add eugeniughelbur/obsidian-second-brain
/plugin install obsidian-second-brain@obsidian-second-brain

That ships all 49 commands, the skill manual, the session-context hook, the opt-in background agent (inert until you arm it - see hooks/postcompact.hook.example.json), and the vault MCP server. Then tell Claude where your vault lives by adding to the env section of ~/.claude/settings.json:

"env": { "OBSIDIAN_VAULT_PATH": "/path/to/your/vault" }

Restart Claude Code, then run /obsidian-second-brain:obsidian-init inside your vault. Plugin commands are namespaced, so every command is /obsidian-second-brain:<name> (type /obsidian-second-brain: to see all 49). Update later with /plugin update obsidian-second-brain.

Classic install (script). Use this if you want the commands as bare names (/obsidian-init, /research, ...) or you are developing the skill and want live edits. One line (clones the skill, installs the slash commands, registers the session-context hook, and offers the research env):

curl -fsSL https://raw.githubusercontent.com/eugeniughelbur/obsidian-second-brain/main/scripts/quick-install.sh | bash

Or step by step:

git clone https://github.com/eugeniughelbur/obsidian-second-brain ~/.claude/skills/obsidian-second-brain
bash ~/.claude/skills/obsidian-second-brain/install.sh
bash ~/.claude/skills/obsidian-second-brain/scripts/setup.sh "/path/to/your/vault"

Cloning it? A star costs you nothing and is how the next person finds this.

No vault yet? Create a ready-to-use one first (folders, templates, boards, dashboards - passes its own health check out of the box):

cd ~/.claude/skills/obsidian-second-brain
uv run python scripts/bootstrap_vault.py --path ~/Documents/MyVault --name "Your Name"
bash scripts/setup.sh ~/Documents/MyVault

Then open Claude Code and run /obsidian-init inside your vault.

Codex CLI / Gemini CLI / OpenCode

Codex and OpenCode users: prefer the Agent Skills build below. The standalone codex-cli and opencode builds are deprecated and superseded by it; both print that notice in their own INSTALL.md. They still work, and will until they are removed. Gemini CLI has no replacement build, so this is the right path there.

git clone https://github.com/eugeniughelbur/obsidian-second-brain
cd obsidian-second-brain
bash scripts/build.sh --platform codex-cli   # or gemini-cli, or opencode
cp -R dist/codex-cli/. /path/to/your/vault/   # or dist/gemini-cli/. or dist/opencode/.

Then start your CLI from the vault root.

The Codex build emits native Codex Agent Skills: one skill per command under .agents/skills/<name>/SKILL.md. Codex discovers them automatically with progressive disclosure (only each skill's name + description load until it's selected), and they run in your current session - invoke one with $<name>, pick it from /skills, or just describe the task and let Codex match it implicitly. AGENTS.md stays as a thin always-on manual (vault conventions + the AI-first rule); there is no routing table to maintain because the skill list is the router. The Gemini / OpenCode builds still emit a GEMINI.md / AGENTS.md dispatcher with an auto-generated routing table to command files under .gemini/ / .opencode/.

Run bash scripts/build.sh with no arguments to build every platform at once. See dist/<platform>/INSTALL.md after building for platform-specific notes.

Google Antigravity (and any .agents/skills/ harness)

Antigravity, Codex CLI, OpenCode, and GitHub Copilot CLI have all converged on the open Agent Skills standard: workspace skills at .agents/skills/<name>/SKILL.md. The agent-skills build emits one spec-compliant tree they all read - and any future harness on the same standard works with zero repo changes.

git clone https://github.com/eugeniughelbur/obsidian-second-brain
cd obsidian-second-brain
bash scripts/build.sh --platform agent-skills

# install with skills.sh (writes one shared .agents/skills/ tree), from your vault root:
npx skills add /path/to/obsidian-second-brain/dist/agent-skills -a antigravity -a codex -a opencode
# or copy manually, no skills.sh required:
cp -R dist/agent-skills/skills/. /path/to/your/vault/.agents/skills/

Each command becomes a skill under .agents/skills/; a shared obsidian-core skill carries the Python toolkit and the AI-first write spec the others call into. The skills are self-sufficient (they resolve the vault root from $OBSIDIAN_VAULT_PATH or the working directory and embed the write spec), so they need no session-start hook. This is the recommended path for Google Antigravity, whose skill discovery differs from classic Gemini CLI: Antigravity still reads the gemini-cli build's GEMINI.md as passive context, but only detects active skills under .agents/skills/, so install this build (not gemini-cli) if you want Antigravity to surface the commands as skills. See dist/agent-skills/INSTALL.md for the full story (skills.sh, manual copy, per-harness notes, and the optional always-on vault-routing rule).

Pi Coding Agent

git clone https://github.com/eugeniughelbur/obsidian-second-brain
cd obsidian-second-brain
bash scripts/build.sh --platform pi
pi install ./dist/pi          # or: cp -R dist/pi/.pi/ /path/to/your/vault/

The Pi build emits a native Pi package: prompt templates under .pi/prompts/ (invoke as /obsidian-save, /obsidian-daily, etc.) plus a discovery skill under .pi/skills/obsidian-second-brain/ (load with /skill:obsidian-second-brain). Pi reads the same ~/.config/obsidian-second-brain/.env keys as the other platforms. It has no background-agent equivalent, and the scheduled agents (obsidian-nightly and the others) are prompts, not commands, so Pi has no /obsidian-nightly to type. To run one, copy its prompt from the scheduled agents section of SKILL.md into a Pi session, by hand or from your own scheduler. (Contributed by @Gepetdo.)

Use it in Grok Bot

Obsidian Second Brain turns what's on your mind into linked notes in your Obsidian vault, keeps your daily notes, and answers your questions from your own notes with links back to the source.

Start from the official Obsidian Second Brain bot template: https://x.ai/bot/Oj_doyprowDl817Yk5Rbh

Grok Bot / Sand

git clone https://github.com/eugeniughelbur/obsidian-second-brain
cd obsidian-second-brain
bash scripts/build.sh --platform grok-bot
# Review dist/grok-bot/INSTALL.md for platform-specific instructions

What you need: a plan that includes Grok Bot. Premium, Super and Ultra on The X Subscription include it, with one weekly usage pool shared with Grok and Cursor. Older paid Cursor plans and linked SuperGrok or X Premium+ accounts work too (https://cursor.com/help/grok-bot/plans).

The Grok Bot build emits workflow SKILL.md files that Grok Bot and Sand agents invoke with / or @. Each skill is a self-contained playbook (name, description, operating instructions). The user-obsidian-second-brain MCP server (already connected in Grok Bot) provides the vault I/O layer via obsidian_* tools (obsidian_search, obsidian_read_note, obsidian_save_note, obsidian_update_note, obsidian_validate_note, etc.). Skills tell the agent which MCP tool to call and how to structure the data. Set $OBSIDIAN_VAULT_PATH to your vault root. No hooks, no scheduled agents - Grok Bot has no hook runtime.

Grok Bot can write a live Page, such as a report, a dashboard, or a plan. The Page opens from a card in the chat, stays in the bot's Library, and you can share it with only you, your team, or anyone with the link. A weekly review or a project dashboard from your vault fits this.

On an iPhone 15 Pro or later, pressing and holding the Action Button starts a voice chat with Grok Bot. You need Grok Bot 1.16 or later, and you set it in iPhone Settings > Action Button > Shortcut. Use it to speak a thought and save it into the vault.

Run on Hermes / open models

The skill is model-agnostic. The OpenCode build (and the Codex / Gemini builds) are plain instruction files, so they run on whatever model the host CLI is pointed at - including open models like Nous Research Hermes. No separate build, no code changes. You set the model on OpenCode's side.

There is also a dedicated Hermes Agent build that emits the commands as native Hermes skills (skills/<category>/<name>/SKILL.md, agentskills.io-compatible), so Hermes discovers and runs them through its own Skills System rather than via a host CLI:

bash scripts/build.sh --platform hermes
# then follow dist/hermes/INSTALL.md (copy into ~/.hermes/skills/ or add as a tap)

Do not run hermes plugins install on this repo's URL. The repo root is not a Hermes plugin (it has no plugin.yaml), and Hermes reports success anyway while registering nothing (#298). Use the skills build above.

This is the skill/playbook half of the Hermes work; the bounded vault-data half is the MCP connector. Native cron and lifecycle-hook integration are tracked in Issue #79.

Point OpenCode at Hermes via OpenRouter. Authenticate once (/connect, search OpenRouter, paste your key - or export OPENROUTER_API_KEY=...), then in opencode.json:

{
  "$schema": "https://opencode.ai/config.json",
  "model": "openrouter/nousresearch/hermes-4-70b",
  "provider": {
    "openrouter": {
      "models": {
        "nousresearch/hermes-4-70b": {}
      }
    }
  }
}

Hermes models on OpenRouter (as of 2026-06, openrouter.ai):

Model id	Best for	Cost (in / out per 1M tokens)
nousresearch/hermes-4-70b	Default. Cheap, capable, 131k context.	$0.13 / $0.40
nousresearch/hermes-4-405b	Strongest instruction-following for the synthesis-heavy commands.	$1.00 / $3.00
nousresearch/hermes-3-llama-3.1-405b:free	Zero-cost trial (needs any OpenRouter key to authenticate).	free

For the privacy story, run a smaller Hermes locally through Ollama or LM Studio and point OpenCode at the local endpoint - no data leaves your machine.

What to expect (open models follow instructions less reliably than Claude, so this is honest, not a promise of parity): the core commands - /obsidian-save, /obsidian-daily, /obsidian-capture, /obsidian-find, /obsidian-task, and /research in free mode - hold up well. The sub-agent-heavy commands and the deep synthesis ones (/obsidian-architect, /obsidian-reconcile, /research-deep) lean hard on instruction-following, so prefer hermes-4-405b (or Claude) for those. The AI-first vault rule still applies on every write regardless of model.

Research toolkit (optional)

The 7 research commands use API keys (2 of them fall back to free sources without any).

Installed the plugin? You have no repo checkout, so install.sh, .env.example, and uv sync are not on your disk. Create the env file by hand instead - the research scripts read this path regardless of how you installed, and the plugin's MCP server already runs under uv run --no-project --with 'mcp<2', so there is nothing to uv sync:

mkdir -p ~/.config/obsidian-second-brain
touch ~/.config/obsidian-second-brain/.env
chmod 600 ~/.config/obsidian-second-brain/.env
# then paste the keys from the table below into that file

On Windows (Git Bash / MSYS2) the file lives under your Windows profile, %USERPROFILE%\.config\obsidian-second-brain\.env: that is where Python (Path.home()), Claude Code, and the bash scripts resolve the home, even when a corporate HOME points at another drive. Bash's own ~ still follows HOME, so on such a machine create the file from USERPROFILE instead of with the commands above:

CONFIG="$(cygpath -u "$USERPROFILE")/.config/obsidian-second-brain"
mkdir -p "$CONFIG" && touch "$CONFIG/.env" && chmod 600 "$CONFIG/.env"

To keep the file anywhere else, set OBSIDIAN_ENV_FILE to its full path; every reader an