obsidian-second-brain turns an Obsidian vault into persistent, searchable memory for Claude Code and other command-line coding agents, storing knowledge as linked Markdown notes. It is for developers, founders, writers, and researchers who want agents to retain project context across sessions. Its catalogue entries provide commands, hooks, a plugin, a skill, and instructions for capturing, finding, and maintaining that memory.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
git clone --depth 1 https://github.com/eugeniughelbur/obsidian-second-brainWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/commands/eugeniughelbur/obsidian-second-brain/obsidian-emerge)<a href="https://agentmods.dev/commands/eugeniughelbur/obsidian-second-brain/obsidian-emerge"><img src="https://agentmods.dev/badge/commands/eugeniughelbur/obsidian-second-brain/obsidian-emerge/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/commands/eugeniughelbur/obsidian-second-brain/obsidian-emerge"><img src="https://agentmods.dev/badge/commands/eugeniughelbur/obsidian-second-brain/obsidian-emerge.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00020 | $0.00865 |
| Opus 5 | $0.00010 | $0.00432 |
| Sonnet 5 | $0.00004 | $0.00173 |
| Haiku 4.5 | $0.00002 | $0.00086 |
Grade A, and why
obsidian-emerge scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
Use the obsidian-second-brain skill. Execute /obsidian-emerge $ARGUMENTS:
The optional argument is a timeframe (e.g., "2 weeks", "this month"). Default: last 30 days.
- Read
_CLAUDE.mdfirst if it exists in the vault root - Determine the date range from the argument (default: last 30 days)
- Spawn parallel subagents to read vault content from the period:
- Daily notes agent: read all daily notes in the date range, extract recurring topics, complaints, observations, and energy patterns
- Dev logs agent: read all dev logs in the range, extract repeated blockers, tools mentioned, architectural patterns
- Decisions agent: read Key Decisions sections across project notes, look for directional trends
- Ideas agent: read notes created in the range in the ideas/concepts folder (resolved per
references/folder-map.md- wiki-stylewiki/concepts/, Obsidian-styleIdeas/), look for thematic clusters
- Merge results and identify:
- Recurring themes: topics that appeared 3+ times without being named as a priority
- Emotional patterns: what energizes vs. drains the user (based on language and context)
- Unnamed conclusions: things the notes imply but never state outright (e.g., "you've mentioned onboarding friction in 4 different projects - this is a systemic issue, not a project-specific one")
- Emerging directions: where the vault suggests the user is heading, even if they haven't committed to it
- Present findings as a structured "Pattern Report" - each pattern gets: the evidence (cited notes), the interpretation, and a suggested action
- Offer to save the pattern report to the ideas/concepts folder (resolved per
references/folder-map.md- wiki-stylewiki/concepts/, Obsidian-styleIdeas/) or a relevant project note; standalone reports usetype: emerge(thinking-tool schema inreferences/ai-first-rules.md), namedYYYY-MM-DD - emerge.md - Log a brief summary in today's daily note
The goal is insight the user cannot see themselves. Do not restate what they already know - surface what they haven't named yet.
AI-first rule: Every note created or updated by this command MUST follow references/ai-first-rules.md - ## For future agent preamble, rich frontmatter (type, date, tags, ai-first: true, plus type-specific fields), recency markers per external claim, mandatory [[wikilinks]] for every person/project/concept referenced, sources preserved verbatim with URLs inline, and confidence levels where applicable. If that path does not resolve from your working directory, search upward for it; if you still cannot read it, say so before writing rather than producing a note that silently skips the rule. The vault is for future agent retrieval - not human reading.
Anti-fabrication: Search exhaustively before claiming any note, person, or file is absent - false absence is the most common failure mode - and never invent facts, entities, or dates (mark unknowns as TBD). See the anti-fabrication and search-completeness hard rules in references/ai-first-rules.md.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 11d ago First seen · 37 lines · 20 tokens per session scan A 5ef1ed1280fd
obsidian-emerge is a command published in the GitHub repository eugeniughelbur/obsidian-second-brain (4,392 stars, last pushed 4d ago), licensed MIT. It adds 20 tokens to every session and 865 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other commands, from other repositories
patterns
Scan recent sessions for recurring patterns and turn them into captures (rules, concept notes, writing seeds).
cierre
A sales call just ended: turn its transcript into the full follow-up (CRM, tasks, email draft, reminder, coaching).
deconstruct
First-principles analyst: surface hidden assumptions, find foundational truths, rebuild from scratch.
instinct-import
Import a portable YAML instinct pack with confidence-gated merge (Instinct Engine).
second-brain-mapping
Map your vault: extract structured metadata from every typed file, surface cross-doc insights, optionally build a knowledge graph.
setup-vault-types
Configure which document types your vault uses (journals, books, meetings, clients, etc.) and scaffold extractors.