/wiki-brain — A Compounding Knowledge Base for Claude Code

Turn Claude Code into a system that remembers. Every conversation feeds an ever-growing personal wiki you browse in Obsidian. Claude queries a knowledge graph before reading raw files, so answers are faster, smarter, and cheaper over time.

Based on Andrej Karpathy's LLM Wiki pattern and powered by Graphify.

Invocation

/wiki-brain                        # first run: setup wizard · after: show status menu
/wiki-brain ingest <file-or-url>   # ingest a new source into the wiki
/wiki-brain query "<question>"     # query the knowledge graph + wiki
/wiki-brain lint                   # health check the wiki
/wiki-brain rebuild                # force a graphify rebuild
/wiki-brain doctor                 # verify install health
/recall                            # show last 5 sessions + read linked pages

Step 0 — First-Time Setup

Check for config at ~/.claude/skills/wiki-brain/config.json. If it exists with setupComplete: true, skip to Step 1 (status menu).

If no config, run the setup wizard.

0.1 — Greet the user

Welcome to /wiki-brain!

This turns Claude Code into a knowledge base that compounds. Every
conversation you have from now on can feed a personal wiki you'll
browse in Obsidian. Claude gets smarter about YOUR stuff over time,
and answers questions faster by querying a knowledge graph instead
of re-reading files.

Setup takes about 5 minutes. Let's go.

0.2 — Ask about Obsidian

Question 1 of 4: Do you already use Obsidian?

Obsidian is a free app for browsing markdown notes with backlinks
and graph view. Your wiki lives inside an Obsidian "vault" (just a
folder on your computer).

  1. Yes — I already have Obsidian installed and a vault set up
  2. No  — I need to install it and create a vault

If answer is 1:

Great. What's the full path to the vault you want to use?

Example: /Users/yourname/Documents/MyVault

(Tip: in Obsidian, right-click your vault name in the sidebar and
choose "Reveal in Finder/Explorer" to see the path.)

Read the path, verify it exists and is writable. If not, ask again.

If answer is 2:

No problem. Here's how to install Obsidian and create a vault:

STEP 1 — Download Obsidian
  • Go to https://obsidian.md
  • Click "Download" and pick your operating system
  • Open the downloaded file and install it (drag to Applications on
    Mac, run the installer on Windows)

STEP 2 — Create a vault
  • Open Obsidian
  • Click "Create new vault"
  • Name it something like "Brain" or "Wiki"
  • Pick a location (Documents folder is a good default)
  • Click "Create"

STEP 3 — Find the vault path
  • In Obsidian, right-click your vault name in the top-left sidebar
  • Click "Reveal in Finder" (Mac) or "Show in Explorer" (Windows)
  • Copy the full path from the Finder/Explorer address bar

Come back here when you've done all three steps. Paste the full
path to your vault and hit Enter.

Wait for the path. Verify it exists and is a directory.

0.3 — Ask about Graphify rebuild cadence

Question 2 of 4: How often should we rebuild your knowledge graph?

WHAT THIS IS:
Graphify reads all your wiki notes and builds a "map" of how
everything connects — which topics relate to which, what links
to what. When you ask Claude a question, it queries this map
first instead of opening every file one by one. This makes
Claude faster, smarter, and cheaper because it doesn't have
to re-read your notes every time.

WHY IT NEEDS REBUILDING:
Every time you finish a Claude conversation, your wiki gets
updated with new info. The map gets a little out of date.
A "rebuild" tells Graphify to re-scan your wiki and update
the map so Claude is working with current information.

IMPORTANT:
A rebuild only runs if your wiki has actually changed since
last time. If nothing's new, it skips. You never burn compute
for nothing.

PICK ONE:
  1. Aggressive  — every 3 days
     Best if you're in Claude Code daily and want the freshest map.

  2. Balanced    — every 7 days          ← recommended
     Good for most people. Stays current week to week.

  3. Manual only — no auto rebuild
     You run /wiki-brain rebuild yourself. Full control, zero
     background activity.

0.4 — Ask about lint cadence

Question 3 of 4: How often should we health-check your wiki?

WHAT THIS IS:
Over time, your wiki accumulates pages. Some get out of date.
Some end up disconnected from everything (orphans). Some say
one thing on page A and the opposite on page B (contradictions).
A "lint" is Claude doing a health check on your wiki — it reads
through, looks for problems, and reports them so you can fix
or ignore them.

WHY IT MATTERS:
A wiki you don't maintain rots. Lint catches rot early. It
doesn't auto-fix anything — you stay in control.

WHAT LINT CHECKS:
  • Contradictions — page A says X, page B says the opposite
  • Stale claims — info that newer notes have superseded
  • Orphan pages — notes nothing else links to
  • Missing pages — concepts mentioned everywhere with no
                    dedicated page
  • Broken links — [[references]] to pages that don't exist

PICK ONE:
  1. Weekly       — for fast-growing wikis
  2. Monthly      — recommended for most people
  3. Manual only  — you run /wiki-brain lint yourself

0.5 — Ask about CLAUDE.md location

Question 4 of 4: Where should I add the wiki-brain instructions?

I need to add a short block of instructions to your CLAUDE.md
so Claude knows how to use your wiki. You can put these in:

  1. Your GLOBAL CLAUDE.md (~/.claude/CLAUDE.md)
     Wiki-brain will work in every project.

  2. A specific project's CLAUDE.md
     Only that project will use the wiki. Paste the path when
     asked.

Pick one:

If 2, ask for the path. Verify the file exists (or offer to create it).

0.6 — Check Graphify is installed

Run:

which graphify 2>/dev/null || python3 -c "import graphify" 2>/dev/null && echo "GRAPHIFY_OK" || echo "GRAPHIFY_MISSING"

If missing:

Installing Graphify now... (this is the tool that builds the
knowledge graph from your wiki files)

Run:

python3 -m pip install graphifyy 2>&1 | tail -3 || python3 -m pip install graphifyy --break-system-packages 2>&1 | tail -3

Verify with python3 -c "import graphify" && echo OK. If it still fails, show the error and stop — tell the user to run pip install graphifyy manually and retry /wiki-brain.

0.7 — Create the vault structure

Inside the user's vault path, create:

<vault>/
├── raw/                    # drop source files here
├── wiki/                   # Claude-maintained pages
│   └── index.md            # catalog of all wiki pages
└── log.md                  # chronological record

Use Bash:

VAULT="<user-provided-path>"
mkdir -p "$VAULT/raw" "$VAULT/wiki"
[ ! -f "$VAULT/wiki/index.md" ] && cat ~/.claude/skills/wiki-brain/templates/index.md > "$VAULT/wiki/index.md"
[ ! -f "$VAULT/log.md" ] && cat ~/.claude/skills/wiki-brain/templates/log.md > "$VAULT/log.md"

0.8 — Preview the CLAUDE.md patch

Show the user exactly what will be added to their CLAUDE.md BEFORE writing anything. Read ~/.claude/skills/wiki-brain/templates/claude-md-patch.md, substitute {{VAULT_PATH}} with the user's vault path, and display:

Here's what I'll add to <CLAUDE.md path>:

---
<rendered patch>
---

Want me to append this? (yes/no)

If no, stop and tell the user they can re-run /wiki-brain later.

If yes, append to the CLAUDE.md file (never overwrite). If the file already has ## Wiki-Brain or ## Context Navigation headers, warn the user and ask before appending to avoid duplicates.

0.9 — Install the SessionEnd hook

Read ~/.claude/settings.json (create it as {} if missing). Add a SessionEnd hook entry that runs the wiki-brain hook script. The hook script path is ~/.claude/skills/wiki-brain/hooks/session-end.sh.

Use this JSON merge pattern (preserve any existing hooks):

{
  "hooks": {
    "SessionEnd": [
      {
        "matcher": "*",
        "hooks": [
          {
            "type": "command",
            "command": "~/.claude/skills/wiki-brain/hooks/session-end.sh"
          }
        ]
      }
    ]
  }
}

Make the hook script executable: chmod +x ~/.claude/skills/wiki-brain/hooks/session-end.sh.

0.10 — Save config

Write ~/.claude/skills/wiki-brain/config.json:

{
  "setupComplete": true,
  "setupDate": "<YYYY-MM-DD>",
  "vaultPath": "<user-provided-path>",
  "claudeMdPath": "<path-they-picked>",
  "rebuildCadenceDays": 3 | 7 | 0,
  "lintCadenceDays": 7 | 30 | 0,
  "lastRebuild": null,
  "lastLint": null
}

0 means manual only.

0.11 — First build

Run the first Graphify build on the (empty) wiki so the output directory exists:

cd "$VAULT" && graphify . --wiki 2>&1 | tail -5 || true

It's OK if this does nothing — the wiki is empty. Just prime the directory.

0.12 — Confirm and end setup

All set. Here's what just happened:

  ✓ Obsidian vault: <path>
  ✓ Folders created: raw/, wiki/, log.md
  ✓ Graphify installed
  ✓ CLAUDE.md patched
  ✓ SessionEnd hook installed
  ✓ Cadence: rebuild every <N> days, lint every <N> days

WHAT TO DO NEXT:
  1. Open Obsidian and point it at your vault
  2. Drop any source (article, PDF, transcript) into <vault>/raw/
  3. Tell Claude: "Ingest the new file in raw/"
  4. Watch your wiki fill up with interlinked pages
  5. Use /recall anytime to see what you've been working on

Your wiki will get richer with every conversation from now on.
Welcome to compounding knowledge.

Step 1 — After Setup: The Status Menu

When /wiki-brain is called with no arguments AND config exists, load the config and show:

Wiki-Brain — <vault-path>

  Pages in wiki:        <count>
  Sources in raw/:      <count>
  Last rebuild:         <date> (next due in N days)
  Last lint:            <date> (next due in N days)
  Log entries:          <count>

WHAT WOULD YOU LIKE TO DO?
  1. Ingest a source        (/wiki-brain ingest <file>)
  2. Query the wiki         (/wiki-brain query "<question>")
  3. Health check           (/wiki-brain lint)
  4. Force rebuild          (/wiki-brain rebuild)
  5. Show recent activity   (/recall)
  6. Diagnose setup         (/wiki-brain doctor)
  7. Exit

Step 2 — Ingest

/wiki-brain ingest <file-or-url>

If it's a URL: fetch content and save as <vault>/raw/<slug>-<date>.md. If it's a local file: copy it into <vault>/raw/ (never modify the original).
Read the source in full.
Summarize the key takeaways for the user (bullet list, 5–10 points). Ask if you should emphasize anything specific.
Write/update wiki pages:
- Create a new page <vault>/wiki/<topic-slug>.md if this is a new topic
- Update existing pages that this source touches
- Add cross-links using [[Other Page]] Obsidian syntax
- Use YAML frontmatter: ---\ndate: <YYYY-MM-DD>\nsources:\n - <filename>\ntags: [...]\n---
Update <vault>/wiki/index.md — add the new page with a one-line summary.

Append to <vault>/log.md:

## [YYYY-MM-DD HH:MM] ingest | <source title>
Touched: wiki/page-a.md, wiki/page-b.md, wiki/page-c.md

Report back: which pages were created, which updated, how many cross-links added.

Be thorough. A single source should typically touch 3–10 wiki pages. That's how the wiki compounds — don't be lazy.

Step 3 — Query

/wiki-brain query "<question>"

Run graphify query "<question>" from the vault directory. This returns a graph-based answer.
Read <vault>/wiki/index.md to find any directly relevant pages the graph query might have missed.
Read those pages.
Synthesize an answer that cites the wiki pages (with [[Page Name]] links).
If the answer itself is valuable, ask: "Want me to file this answer back into the wiki as a new page?" If yes, create <vault>/wiki/<topic>-analysis-<date>.md and update the index.

Append to log:

## [YYYY-MM-DD HH:MM] query | "<question>"
Answered from: <pages>

Step 4 — Lint

/wiki-brain lint

A health-check pass. Claude reads the wiki and reports problems.

Read <vault>/wiki/index.md to get all pages.
Sample up to 30 pages (or all, if fewer).
Check for:
- Contradictions — pages that assert incompatible facts
- Stale claims — older pages superseded by newer ones
- Orphans — pages with zero inbound [[links]]
- Missing pages — concepts referenced across 3+ pages with no dedicated page
- Broken links — [[Target]] where Target doesn't exist
- Gaps — topics where a web search or new source would add value
Write a report to <vault>/lint-reports/<YYYY-MM-DD>.md.
Display a summary: counts per category + top 5 issues.
Ask which issues (if any) to fix now. Do NOT auto-fix.
Update lastLint in config.
Append to log.

Step 5 — Rebuild

/wiki-brain rebuild

Force a Graphify rebuild.

cd "$VAULT" && graphify . --wiki --update 2>&1 | tail -10

Update lastRebuild in config. Report success or failure.

Step 6 — Doctor

/wiki-brain doctor

Verify install health. Run these checks and report pass/fail for each:

config.json exists and is valid JSON
Vault path exists and is writable
raw/, wiki/, wiki/index.md, log.md all exist
graphify is importable (python3 -c "import graphify")
SessionEnd hook is in ~/.claude/settings.json
session-end.sh is executable
CLAUDE.md contains the wiki-brain block
Last rebuild was within rebuildCadenceDays × 2 (warn if older)
log.md has at least one entry in the last 30 days (warn if not)

Display results as a checklist. For any failure, show the exact fix.

Step 7 — Recall

/recall

Run tail -20 "<vault>/log.md" to get recent entries.
Parse the last 5 session/ingest/query entries.
For each, read the wiki pages it touched (linked in the log line).

Display a summary:

Last 5 activities:

1. [2026-04-11 15:45] ingest | "The LLM Wiki Pattern"
   Touched: [[LLM Wikis]], [[Karpathy Principles]], [[Graphify]]

2. [2026-04-10 09:12] query | "how do we ingest conversations?"
   Answered from: [[LLM Wikis]], [[SessionEnd Hooks]]
...

Ask: "Want me to load the full content of any of these into context?"

Session-End Behavior (What Claude Must Do Before Ending a Session)

When the user ends a Claude Code session and this skill is active, Claude must:

Append one line to <vault>/log.md in the format:

## [YYYY-MM-DD HH:MM] session | <3-8 word session title>
Touched: <comma-separated wiki pages OR "none">

If anything durable happened (decisions made, things learned, project state changed, problems solved): update or create relevant wiki pages with that knowledge. Same rules as /wiki-brain ingest — cross-link, update the index, be thorough.
If nothing durable happened (trivial task, one-off question): skip the wiki update. Just log the line.

This is instructed in the CLAUDE.md patch. The SessionEnd hook runs AFTER this and handles Graphify rebuild cadence checks.

Rules

Never modify files in raw/. Sources are immutable.
Claude owns wiki/ entirely. The user doesn't edit it (except for the occasional correction).
Always update wiki/index.md when creating or renaming a page.
Always append to log.md on ingest, query, lint, rebuild, and session end.
Cross-link aggressively. Use [[Page Name]] Obsidian syntax. A page with no links is a dead-end.
Short pages are fine. A wiki page can be 3 lines. What matters is the links, not the length.
Contradictions get flagged, not silently resolved. If a new source contradicts an existing page, note it in the page with > Contradicts: <older claim, source> and let the user decide.
Never auto-fix during lint. Report issues, ask before fixing.
Respect cadence-manual. If the user picked "manual only" for rebuild or lint, the hook must skip it.
Privacy: config.json is gitignored. The vault is the user's private space — never commit it or send it anywhere.

Built by @tenfoldmarc. Follow for daily AI automation builds — real systems, not theory.