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-reconcile)<a href="https://agentmods.dev/commands/eugeniughelbur/obsidian-second-brain/obsidian-reconcile"><img src="https://agentmods.dev/badge/commands/eugeniughelbur/obsidian-second-brain/obsidian-reconcile/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-reconcile"><img src="https://agentmods.dev/badge/commands/eugeniughelbur/obsidian-second-brain/obsidian-reconcile.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 | $0.00014 | $0.01028 |
| Opus 5 | $0.00007 | $0.00514 |
| Sonnet 5 | $0.00003 | $0.00206 |
| Haiku 4.5 | $0.00001 | $0.00103 |
Grade A, and why
obsidian-reconcile 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-reconcile $ARGUMENTS:
The optional argument is a topic or entity to focus on. If not provided, scan the whole vault.
-
Read
_CLAUDE.mdfirst if it exists in the vault root -
Read
index.mdto understand the full vault landscape -
Spawn parallel subagents to find contradictions:
- Claims agent: scan the concepts and projects folders (resolved per
references/folder-map.md) for factual claims - find pairs that contradict each other - Entity agent: scan the entities folder (resolved per
references/folder-map.md) for outdated roles, companies, or descriptions that conflict with newer sources - Decisions agent: scan the decisions folder (resolved per
references/folder-map.md) and project Key Decisions for reversed or superseded decisions that were never updated - Source freshness agent: compare
raw/source dates againstwiki/page dates - flag wiki pages that reference old sources when newer ones exist on the same topic
- Claims agent: scan the concepts and projects folders (resolved per
-
For each contradiction found, evaluate:
- Which source is newer? (date comparison)
- Which source is more authoritative? (peer-reviewed > blog post > transcript > opinion)
- Is this a genuine contradiction or an evolution? (someone changing their mind is not a contradiction - it's growth)
-
Resolve each contradiction:
- Clear winner: rewrite the outdated page with current info. Add a
## Historysection noting what changed and why: "Previously stated X (source: raw/articles/old-article.md, 2025-11-01). Updated to Y based on newer evidence (source: raw/articles/new-article.md, 2026-03-15)." - Genuinely ambiguous: create
Conflict - Topic.mdin the decisions folder (resolved perreferences/folder-map.md;type: conflict, schema inreferences/ai-first-rules.md) documenting both sides, the evidence for each, and mark asstatus: openfor the user to decide - Evolution: update the entity/concept page to reflect the current state and add the historical context
- Clear winner: rewrite the outdated page with current info. Add a
-
After all resolutions:
- Rebuild affected sections of
index.md - Append to the operation log: if
Logs/exists write**HH:MM** - reconcile | X contradictions found, Y auto-resolved, Z flagged for usertoLogs/YYYY-MM-DD.md; otherwise append## [YYYY-MM-DD] reconcile | X contradictions found, Y auto-resolved, Z flagged for usertolog.md - Update today's daily note with a reconciliation summary
- Rebuild affected sections of
-
Report back:
- Auto-resolved (list with old claim → new claim and why)
- Flagged for user (genuinely ambiguous - needs human judgment)
- Stale pages updated (pages rewritten with fresher sources)
The vault should never contain two pages that disagree without knowing they disagree. Contradictions are either resolved or explicitly documented as open questions.
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 · 50 lines · 14 tokens per session scan A 0e5cf7eacb01
obsidian-reconcile is a command published in the GitHub repository eugeniughelbur/obsidian-second-brain (4,392 stars, last pushed 4d ago), licensed MIT. It adds 14 tokens to every session and 1,028 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.