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-init)<a href="https://agentmods.dev/commands/eugeniughelbur/obsidian-second-brain/obsidian-init"><img src="https://agentmods.dev/badge/commands/eugeniughelbur/obsidian-second-brain/obsidian-init/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-init"><img src="https://agentmods.dev/badge/commands/eugeniughelbur/obsidian-second-brain/obsidian-init.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 | $0.00022 | $0.01258 |
| Opus 5 | $0.00011 | $0.00629 |
| Sonnet 5 | $0.00004 | $0.00252 |
| Haiku 4.5 | $0.00002 | $0.00126 |
Grade A, and why
obsidian-init 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 9d 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.
How it starts
The opening of the file, as written. The whole thing — 55 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Use the obsidian-second-brain skill. Execute /obsidian-init:
-
Glob the vault (
<vault>/**/*.md) to map the full vault structure -
Spawn parallel subagents to discover vault context simultaneously:
- Dashboard agent: read
Home.mdor equivalent dashboard - Templates agent: read all files in
Templates/ - Boards agent: read all files in
Boards/ - Samples agent: read one existing note per major folder to capture naming conventions and frontmatter patterns
- Dashboard agent: read
-
Merge all agent results into a complete picture of the vault
-
Generate a complete
_CLAUDE.mdusing the template bundled with the skill atSKILL_ROOT/references/claude-md-template.md(its absolute path was given at session start as Skill root), filled with real values from the vault -
Generate
index.mdat the vault root - a catalog of all pages organized by category:- List every note in the vault grouped by folder (Projects, People, Ideas, etc.)
- Include a one-line description for each note (from frontmatter or first paragraph)
- Claude reads this file FIRST when navigating the vault - cheaper and faster than searching
- Format:
- [[Note Name]] - brief description
-
Initialize the vault operations log:
- Create
Logs/directory at the vault root - Write
log.mdat the vault root as a thin pointer file: explains the per-day structure, points atLogs/, and ships the entry template (do NOT put log entries inlog.mditself) - Write today's
Logs/YYYY-MM-DD.mdwith the init entry:**HH:MM** - init | Vault initialized with _CLAUDE.md, index.md, Logs/ - Per-day file format: frontmatter (
type: log,date,ai-first: true) +**HH:MM** - action | descriptionentries, append-only
- Create
-
Create
Bases/at the vault root if it does not exist. Stamp the four premade base files fromSKILL_ROOT/references/bases/(the skill root given at session start):Template Output file Obsidian-style folder Wiki-style folder projects.base.templateBases/Projects.baseProjectswiki/projectspeople.base.templateBases/People.basePeoplewiki/entitiestasks.base.templateBases/Tasks.baseTaskswiki/tasksdaily.base.templateBases/Daily.baseDailywiki/dailyDetect vault style from the folder structure discovered in step 1: if
wiki/exists at the root, use wiki-style folder names; otherwise use obsidian-style. For each template, replace its named placeholder ({{DAILY_FOLDER}},{{PEOPLE_FOLDER}},{{PROJECTS_FOLDER}},{{TASKS_FOLDER}}) with the correct folder name, then write toBases/.Skip any base file that already exists in
Bases/- never overwrite. -
Write
_CLAUDE.md,index.md, rootlog.md(pointer),Logs/YYYY-MM-DD.md(today's entries), and any newBases/*.basefiles -
Confirm what was written and tell the user to restart their Claude session so the new files take effect
If _CLAUDE.md already exists: show a diff of what would change and ask before overwriting.
If index.md already exists: regenerate it (it's always a fresh catalog of current vault state).
If a monolithic log.md already exists with ## YYYY-MM-DD sections: run uv run --directory "SKILL_ROOT" scripts/migrate_log.py --vault <vault-path> (its absolute path was given at session start as Skill root; substitute it for SKILL_ROOT) to split it into Logs/YYYY-MM-DD.md files. Do not overwrite manually.
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.
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.
- 9d ago First seen · 55 lines · 22 tokens per session scan A 53a5645ec40e
obsidian-init is a command published in the GitHub repository eugeniughelbur/obsidian-second-brain (4,364 stars, last pushed 2d ago), licensed MIT. It adds 22 tokens to every session and 1,258 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.
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