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🧠 claude-obsidian-kit

LLM wiki kit

First committed by selmakcby

Published in selmakcby/claude-obsidian-kit. Publisher page

26 GitHub stars

What it is

Give your Claude Code agents a shared, persistent brain β€” an Obsidian vault that survives sessions. Includes a retrofit guide for folders you already have, and a runnable vault linter.
β€” the description by selmakcby

AutoGineer overview, from the brain’s own files

claude-obsidian-kit transforms ephemeral Claude Code sessions into a persistent knowledge base. By introducing specialized agentsβ€”the archivist for reading and linting, and the scribe for writingβ€”it enables agents to maintain context across sessions. The kit provides a structured vault template, a schema-driven constitution, and a linter to ensure the integrity of the knowledge graph, effectively turning a project's reasoning into a searchable, long-term asset.

How it works

Memory model: LLM wiki

AutoGineer overview, from the brain’s own files

The kit installs two specialized agents into your project: an archivist that handles queries and vault health, and a scribe that performs efficient writes. It uses a structured Obsidian vault layout with predefined folders for architecture, decisions, design, entities, and concepts. Agents follow a specific llm-wiki skill protocol for ingesting information, querying the vault, and linting for issues like broken links or orphans. A provided Python script allows for command-line linting of the vault's health.

Folders
FolderRoleFiles
agentsagent-instructions2
scriptsscripts2
skillsagent-instructions4
obsidianfolder3
vault-templatefolder10

Requirements

Databases: PostgreSQL

Set it up

  1. This brain runs code automatically: 1 script. Review scripts/install.sh before opening the folder in Claude Code. No step below turns a hook on for you.

    • scripts/install.sh: sh scripts/install.sh
  2. Download the brain as a ZIP and unzip it where you keep your notes or project: https://mp-staging.autogineer.com/agent-brains/selmakcby/claude-obsidian-kit/download
  3. cd claude-obsidian-kit && claude

  4. AutoGineer scanned these files at commit 2826401.

  5. Not scanned by AutoGineerThe author’s README also describes installing it from a clone of its repository. Read its install section: AutoGineer did not scan that path. https://github.com/selmakcby/claude-obsidian-kit/blob/282640137e4761c5a6b0aa75aa509cf39199d6c4/README.md#install
  6. First committed by selmakcby. Published in selmakcby/claude-obsidian-kit. Licence: MIT License.

Usage

AutoGineer overview, from the brain’s own files

  • Automating the ingestion of project decisions into a persistent vault.
  • Querying past architectural decisions to inform current development.
  • Running automated health checks on the knowledge base to identify stale notes or broken links.
  • Maintaining a shared knowledge graph that survives individual agent sessions.
β€œWhy did we choose Stripe webhooks for the payment integration?”
The archivist agent reads the relevant decision note from the vault and synthesizes the rationale in seconds.
β€œCheck vault health.”
The archivist scans the vault for orphans, broken links, and contradictions, returning a severity-sorted report.

Documentation by selmakcby

<div align="center">

🧠 claude-obsidian-kit

Give your Claude Code agents a shared, persistent brain.

Turn ephemeral sessions into accumulating knowledge β€” stored in an Obsidian vault. Built for efficiency: right model for each job, cheap writes, index-first reads.

   β”Œβ”€ planner (opus) ─┐
   β”‚ ui-agent (sonnet)β”‚      QUERY / LINT
   β”‚ builder  (sonnet)β”‚ ─────▢ archivist (sonnet Β· read-only)
   β”‚ reviewer (sonnet)β”‚             β”‚
   β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜             β–Ό
            β”‚                     VAULT
            └────── INGEST ──▢ scribe (haiku Β· writes)
                                     β–²
                                     β”‚
                               Main Claude
                               (orchestrator)

Install Β· Retrofit Β· Lint Β· Efficiency Β· FAQ Β· Prompts πŸ‡ΉπŸ‡·

</div>


What this is

A drop-in kit that extends Claude Code with:

  • Two agents:

    • archivist β€” vault reader + health guardian (QUERY, LINT)

    • scribe β€” dedicated vault writer (INGEST, runs on haiku for efficiency)

  • One skill β€” llm-wiki β€” the INGEST Β· QUERY Β· LINT protocols

  • One constitution β€” vault-template/CLAUDE.md β€” the schema every agent reads before touching the vault (πŸ‡ΉπŸ‡· TΓΌrkΓ§e)

  • One vault template β€” pre-structured Obsidian vault with conventions

  • One linter β€” vault-lint.py, the LINT protocol as a runnable command (no dependencies)

  • One retrofit guide β€” RETROFIT.md, for when you already have months of material

  • Obsidian config β€” graph colours by layer, and the [!conflict] callout the skill needs

After install, your agents read from and write to a shared markdown knowledge graph that survives sessions. Yesterday's decisions are tomorrow's context.


The problem this solves

Default Claude Code agents are stateless:

Monday:  agents plan a feature, build it β†’ close session
Tuesday: new session β€” "why did we use Stripe webhooks?"
Claude:  "I don't know. Let me re-analyze from scratch..."

Every session starts from zero. Context dies with the conversation. The project's reasoning evaporates even when the code persists.

With this kit:

Monday:  agents plan β†’ scribe files to vault/decisions/
Tuesday: "why Stripe webhooks?"
archivist β†’ reads vault/decisions/2026-04-21-stripe-webhooks.md β†’ answers in 1 second with full rationale

Install

Quick
git clone https://github.com/selmakcby/claude-obsidian-kit ~/claude-obsidian-kit

cd ~/claude-obsidian-kit
./scripts/install.sh ~/my-project

Installs:

  • ~/my-project/.claude/agents/archivist.md

  • ~/my-project/.claude/agents/scribe.md

  • ~/my-project/.claude/skills/llm-wiki/

  • ~/my-project/vault/ (if doesn't exist)

Final step

Update your project's CLAUDE.md with vault permissions:

{
  "permissions": {
    "allow": [
      "Write(vault/**)",
      "Edit(vault/**)",
      "Read(vault/**)"
    ]
  }
}

How it works

The 6-agent team

After this kit, your full team:

AgentRoleModelWhy this model
plannerArchitecture + planningopusDeep reasoning
ui-agentDesign + componentssonnetBalanced
builderBackend implementationsonnetCoding quality
reviewerQuality + securitysonnetThorough analysis
archivistVault reads (QUERY, LINT)sonnetSynthesis + audit
scribeVault writes (INGEST)haikuCheap + fast

The scribe / archivist split is token-efficient by design β€” see EFFICIENCY.md.

Three operations
🟒 INGEST (scribe)

Other agents produce findings. Main Claude passes findings to scribe. Scribe formats into proper note + writes to correct folder + updates index.

planner: "We should use monthly/annual pricing toggle"
  ↓
main Claude: Task(scribe, finding="...", type=decision)
  ↓
scribe: writes vault/decisions/2026-04-23-pricing-toggle.md
πŸ”΅ QUERY (archivist)
you: "Why did we choose monthly/annual toggle?"
  ↓
archivist: reads index.md β†’ greps "toggle" β†’ reads 2-3 notes β†’ synthesizes answer
🟑 LINT (archivist)
you: "Check vault health"
  ↓
archivist: scans for orphans, broken links, stale notes, contradictions
archivist: returns severity-sorted report with fix suggestions

Retrofit β€” you already have a folder

vault-template/ assumes you are starting clean. Almost nobody is. The realistic situation is months of accumulated material β€” transcripts, drafts, half-finished projects, and often an older vault somewhere inside that already works.

RETROFIT.md is the guide for that case. It covers the two decisions you make before writing anything (the vault root is the folder you already have; an existing vault inside it is canonical and read-only), and the parallel-ingest design that keeps agents from writing the same entity page twice:

Phase 1  domain agents ──▢ project + decision pages only
                           (reference [[entities]], write none)
              β”‚
              β–Ό  union + dedupe + deterministic split, in code
Phase 2  node agents  ──▢ disjoint slices of the entity/concept list
              β”‚
              β–Ό
Phase 3  index + lint ──▢ one owner for index.md, one audit

Splitting by page type rather than only by domain makes collisions impossible by construction rather than by instruction. Reference run: 1.9 GB, ~1,000 text files, 226 pages, 3,484 links, zero broken links, zero fabricated source citations.


Lint, as a command

skills/llm-wiki/lint.md specifies the checks and a health-score formula. vault-lint.py implements that spec so the result is measured rather than asserted. Single file, standard library only, read-only:

python3 scripts/vault-lint.py path/to/vault

# retrofit case: audit the wiki layer, resolve links against the whole folder
python3 scripts/vault-lint.py . --notes 'wiki/*' --notes 'index.md'

# non-English frontmatter
python3 scripts/vault-lint.py . --fields tur,durum,guncelleme --date-field guncelleme

# CI
python3 scripts/vault-lint.py . --fail-under 85
CheckWhy it earns its place
Broken linksCode spans are stripped first β€” an [[example]] inside backticks is not a broken link
OrphansEntry points (index, log, README) are exempt
Unverifiable sourcesEvery path a note cites in source: is checked against disk. This is how you catch a citation the agent invented
Ambiguous targetsTwo files sharing a basename means [[name]] resolves by proximity β€” possibly not the file you meant
Missing concept pagesA link referenced 3+ times with no page behind it
Frontmatter, stale notesPer the schema; stale = old date still in draft

Flagged > [!conflict] callouts are reported but not scored. A marked contradiction is the protocol working; the dangerous one is unmarked, and no linter can see that. Pass --score-conflicts for the strict formula.


Obsidian config

The skill tells the agent to flag contradictions with > [!conflict] β€” and Obsidian has no such callout type, so they render as anonymous grey notes. obsidian/ fixes that and colours the graph by layer. Copy it into your vault's .obsidian/.


Efficiency

This kit is intentionally designed for low token cost. See EFFICIENCY.md for all 10 patterns.

Highlights:

  • Separate thinking from writing β€” opus plans, haiku files (80% cost reduction on writes)

  • Index-first reads β€” never grep the whole vault

  • Model tiering β€” haiku for scribe, sonnet for reads, opus for architecture

  • Least-privilege tools β€” smaller system prompts, fewer wasted calls

  • Parallel when independent β€” wall-clock savings

Rough cost per full feature (plan + design + build + review + 2 ingests): ~$0.18 Naive "opus everywhere" alternative: ~$0.90 β†’ 5Γ— cheaper with proper model routing.


FAQ

Common questions about INGEST, QUERY, LINT, PII, versioning, RAG comparison, and more β€” see FAQ.md.


Vault layout

vault/
β”œβ”€β”€ index.md              ← entry point, read first
β”œβ”€β”€ _schema/
β”‚   β”œβ”€β”€ template.md       ← required frontmatter for all notes
β”‚   └── conventions.md    ← naming, linking, tagging rules
β”‚
β”œβ”€β”€ architecture/         ← how the system is built
β”œβ”€β”€ decisions/            ← why we chose X over Y (dated)
β”œβ”€β”€ design/               ← UI/UX decisions
β”œβ”€β”€ entities/             ← tools, services (stripe, supabase)
β”œβ”€β”€ concepts/             ← cross-cutting ideas
└── sessions/             ← dated session summaries

Every note has frontmatter. Every note links to others. Orphans are tech debt.


File structure

claude-obsidian-kit/
β”œβ”€β”€ README.md                 ← you are here
β”œβ”€β”€ RETROFIT.md               ← pointing the kit at a folder you already have
β”œβ”€β”€ EFFICIENCY.md             ← token patterns (10 of them)
β”œβ”€β”€ FAQ.md                    ← common questions
β”œβ”€β”€ LICENSE                   ← MIT
β”œβ”€β”€ agents/
β”‚   β”œβ”€β”€ archivist.md          ← reader/guardian (QUERY + LINT)
β”‚   └── scribe.md             ← dedicated writer (INGEST)
β”œβ”€β”€ skills/
β”‚   └── llm-wiki/
β”‚       β”œβ”€β”€ SKILL.md          ← main skill manifest
β”‚       β”œβ”€β”€ ingest.md         ← INGEST protocol detail
β”‚       β”œβ”€β”€ query.md          ← QUERY protocol detail
β”‚       └── lint.md           ← LINT protocol detail
β”œβ”€β”€ vault-template/
β”‚   β”œβ”€β”€ index.md              ← vault entry point
β”‚   β”œβ”€β”€ _schema/
β”‚   β”‚   β”œβ”€β”€ template.md       ← note template
β”‚   β”‚   └── conventions.md    ← full rulebook
β”‚   β”œβ”€β”€ architecture/
β”‚   β”œβ”€β”€ decisions/
β”‚   β”œβ”€β”€ design/
β”‚   β”œβ”€β”€ entities/example-service.md
β”‚   β”œβ”€β”€ concepts/example-concept.md
β”‚   └── sessions/
β”œβ”€β”€ obsidian/
β”‚   β”œβ”€β”€ graph.json            ← graph coloured by vault layer
β”‚   β”œβ”€β”€ snippets/
β”‚   β”‚   └── vault-layers.css  ← [!conflict] callout + folder colours
β”‚   └── README.md
└── scripts/
    β”œβ”€β”€ install.sh            ← one-command setup
    └── vault-lint.py         ← runs the LINT protocol for real (no deps)

Works well with

  • Claude Code β€” the primary target

  • Obsidian β€” the vault viewer/editor (optional β€” vault is plain markdown)

  • VS Code, Typora, Bear β€” any markdown editor works

  • Previous kit: knowledge-pipeline β€” this extends it with the multi-agent efficiency layer


License

MIT


Credits

Built on Claude Code's agent + skill system.

Inspired by:

FAQ.md

FAQ β€” INGEST / QUERY / LINT

Common questions from Video 1 comments + Discord + issues.


INGEST

Q: How often should I run INGEST?

Not manually β€” it happens automatically whenever a decision is made.

  • Planner makes a decision β†’ main Claude calls scribe to INGEST it

  • Builder completes a feature β†’ main Claude calls scribe to file a session note

  • Reviewer finds a pattern worth remembering β†’ main Claude calls scribe

Frequency is: every time knowledge is produced. Not scheduled.

Q: Can I INGEST multiple things at once?

Yes. Main Claude should call scribe multiple times in parallel (single message, N calls).

Main: [Task(scribe, finding=plan), Task(scribe, finding=brief), Task(scribe, finding=review)]
β†’ all 3 notes written in ~5 seconds
Q: What if two agents INGEST conflicting info?

This is where LINT helps. The archivist will flag contradictions as CRITICAL.

Workflow when it happens:

  1. LINT catches two notes saying opposite things

  2. Main Claude asks you (the human) which is correct

  3. Mark the losing one status: deprecated with deprecated_by: [[winner]]

  4. Never delete β€” deprecated notes preserve history

Q: Should I INGEST exploratory thoughts or only final decisions?

Only final decisions. Scribe is for persisting settled knowledge. If you're still thinking out loud, don't file it β€” it'll pollute the vault with noise.

Rule: if you'd change it tomorrow, don't INGEST it yet.

Q: Does INGEST update the index automatically?

Yes β€” scribe appends a one-line entry to index.md when a significant note is added.

"Significant" means it introduces a new top-level concept. Not every decision note gets indexed (that would bloat the index). Only the ones that reshape understanding.

Q: What frontmatter fields are required?
type:   required Β· one of: decision | session | entity | concept | architecture | design
date:   required Β· YYYY-MM-DD
tags:   required Β· can be empty [] but must exist
status: required Β· one of: draft | accepted | deprecated
source: required Β· e.g. "planner", "user", "external-doc"

Optional:

  • links: [[note1]], [[note2]] β€” declares dependencies

  • deprecated_by: [[new-note]] β€” for deprecated notes only

Q: Can INGEST fail / skip?

Scribe will refuse to write if:

  • The file at the target path already exists (collision)

  • It detects an obvious secret in the content (looks like an API key)

  • Required frontmatter can't be constructed from input

In these cases, it flags to main Claude β€” the human decides what to do.


QUERY

Q: Does QUERY read the whole vault?

No β€” that would be expensive and slow. Archivist uses an index-first approach:

  1. Read index.md (your map)

  2. Grep for keywords

  3. Read 2-5 most relevant notes

If a question requires reading 10+ notes, the question is too broad. Narrow it down.

Q: What's the token cost of a typical QUERY?
  • Input: ~2,000 tokens (index + 3 notes read)

  • Output: ~500 tokens (synthesized answer)

  • Model: sonnet

  • Cost: ~$0.01 per QUERY

Cheap enough to run constantly.

Q: Does archivist remember previous QUERYs?

Within the same session, yes (main Claude's context retains it). Across sessions, no β€” each session starts fresh.

But! If a QUERY produces a valuable synthesis, archivist recommends calling scribe to refile it as a concept note. Then next session's QUERY finds the synthesis pre-made.

This is the accumulation loop β€” discoveries turn into assets.

Q: Can QUERY be wrong / hallucinate?

Yes, like any LLM output. Mitigations baked into this kit:

  1. Citations required β€” archivist always links to the source notes it read

  2. Small read scope β€” only 2-5 notes, easy to verify

  3. Synthesized in own words β€” no raw copy-paste (auditable)

When in doubt: click the citations and verify.

Q: What if the vault doesn't have the answer?

Archivist returns:

## Answer
I don't have enough information in the vault to answer this.

## What I looked at
- vault/index.md
- vault/decisions/*.md (grep "X" β€” no matches)
- vault/concepts/*.md (grep "X" β€” no matches)

## Suggestion
This topic might warrant INGESTion. Consider calling scribe after we
research it externally.

No hallucination. Empty answer is an honest answer.


LINT

Q: How often should I LINT?

Weekly is a good default. After a week of work, there are usually:

  • 1-2 orphans

  • 0-1 broken links

  • Some stale notes

More often = nitpicky. Less often = debt accumulates.

Q: Does LINT fix things automatically?

No. LINT is read-only. It reports issues with suggested fixes, but doesn't execute them.

Why? Because most "fixes" need judgment:

  • Orphan note β†’ maybe archive? or link it to parent?

  • Stale note β†’ mark accepted? or deprecate?

Scripts that auto-fix lead to data loss. Humans decide.

Q: What's a good "health score"?
  • 90-100: excellent, stay here

  • 75-89: normal, has some drift

  • 60-74: attention needed, schedule a cleanup

  • < 60: debt is real, half a day of cleanup

Don't chase 100. The cost of perfection isn't worth it. 85 is great.

Q: Can I customize what LINT checks?

Yes β€” edit skills/llm-wiki/lint.md. That's the protocol archivist follows. Add/remove checks, adjust severity weights, change the health score formula.


General

Q: Can I use this without Obsidian?

Yes β€” the vault is just markdown files. You can:

  • Use VS Code instead

  • Use Typora, Bear, or any editor

  • Browse via cat + grep in terminal

Obsidian adds:

  • Backlink visualization

  • Graph view

  • Tag pane

  • Quick switcher (⌘O)

All useful but not required. The system works on raw markdown.

Q: How big can the vault get?

Practically unlimited. Tested with 5,000-note vaults.

Token efficiency matters at scale:

  • 1,000 notes: any QUERY works fine

  • 5,000 notes: index-first + folder-scoped Grep becomes important

  • 10,000+ notes: consider pre-filtering by tag before Grep

Q: What about PII (personally identifiable info)?

Don't INGEST PII. If:

  • User names, emails, IPs β†’ skip

  • Internal project names that might leak β†’ be cautious

  • API keys, secrets β†’ NEVER

scribe has a rule to flag likely-secret patterns. If you INGEST something with a suspected key, scribe refuses and asks main Claude.

Q: Versioning β€” what if I change my mind about a decision?

Workflow:

  1. Old decision: status: accepted β†’ status: deprecated

  2. Add frontmatter field: deprecated_by: [[new-decision-note]]

  3. New decision: ## Replaces\n- [[old-decision-note]]

  4. Never delete. History is context.

Future QUERYs will see both, know the current one, understand the history.

Q: How does this compare to RAG (retrieval-augmented generation)?

RAG: embeddings + vector DB, rediscovers context each query.

This kit: explicit markdown + links, accumulates context.

When to use RAG: large external docs, semantic search over unstructured content.

When to use this kit: project-specific knowledge, decisions, rationale β€” anything you want a human in the loop for.

They can coexist. This kit for your project brain, RAG for "all of Stack Overflow".

Q: Can multiple projects share a vault?

Technically yes, but not recommended. Agents work better when scoped to one project's vault.

Better pattern: each project has its own vault/ inside its repo.

Q: What if I don't want archivist to read my whole index?

Add a visibility: internal frontmatter field to notes you want skipped. Archivist's prompt can be updated to honor it (edit archivist.md).

31 files

Advantages

  • Reduces token costs by using specialized models for different tasks, such as using Haiku for writes and Sonnet for reads. evidence: README.md
  • Ensures knowledge persists across sessions, preventing the loss of project reasoning. evidence: README.md
  • Provides a robust linting protocol to maintain vault health and catch fabricated citations. evidence: README.md

Limitations

  • Requires manual setup and integration into existing project structures. evidence: README.md
  • Relies on specific agent roles which must be correctly configured within the Claude Code environment. evidence: README.md

Security

Risk level: Low risk

This brain runs

Install scripts (1)

  • scripts/install.sh: sh scripts/install.sh
  • Low risk: scripts-present (scripts/install.sh)

Attribution and licence

First committed by
GitHub avatar of selmakcbyselmakcby
Publisher
selma (Community)
Source
selmakcby/claude-obsidian-kit Β· commit 2826401
Licence
MIT License (files served here)
  • ATTRIBUTION.md (written by AutoGineer)
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Contributors
selmakcby

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