four-layer-init

name	four-layer-init
description	Bootstrap a new project with the full 4-layer memory architecture (Pinecone + Obsidian Wiki + GitNexus + CLAUDE.md). Use when user says "setup 4-layer for <project>", "add memory architecture", "onboard <project> to memory ecosystem", "init memory for new project", or similar. Creates reproducible infrastructure that cuts session startup tokens 40-180x across projects.

Four-Layer Memory — Project Bootstrap

Reference architecture: {{RESEARCH_PATH}}\Claude Code Resurch\wiki\concepts\Graphify-vs-GitNexus.md Session protocol: ~/.claude/references/session-start.md

Goal: Apply the 4-layer memory stack to ANY project so every session starts with ~5k tokens instead of 400k+.

When to Invoke

Trigger on phrases like:

• "Setup 4-layer for StroyOffice"
• "Onboard to memory architecture"
• "Init GitNexus + Pinecone for "
• "Apply the memory ecosystem"

Prerequisites Check (run BEFORE onboarding)

# 1. GitNexus installed globally?
gitnexus --version   # should return 1.6.1+

# 2. Pinecone credentials in ~/.claude/.env?
test -f ~/.claude/.env && grep -q PINECONE_API_KEY ~/.claude/.env && echo OK || echo MISSING

# 3. Pinecone wrapper script present?
test -f ~/.claude/scripts/pinecone.py && echo OK || echo MISSING

If any MISSING → see "Initial global setup" at the bottom.

The 7-Step Project Onboarding

Step 1 — Project path + name (ask user)

Project path:   {{CODE_PATH}}\<ProjectName>
Wiki path:      {{WIKI_PATH}}\<ProjectName>\wiki
Pinecone ns:    <ProjectName>           (case-exact, matches folder name)

Step 2 — GitNexus analyze + verify

cd "{{CODE_PATH}}\<ProjectName>"
gitnexus analyze    # ~1-2 min depending on size
gitnexus status     # must show ✅ up-to-date
gitnexus list       # verify project appears in global registry

Expected output: N nodes + M edges. For most projects: 5k–50k nodes.

Step 3 — Git post-commit hook (auto re-index)

cat > .git/hooks/post-commit << 'EOF'
#!/bin/sh
# Auto re-index GitNexus graph after each commit (async, non-blocking).
command -v gitnexus >/dev/null 2>&1 || exit 0
(
  cd "$(git rev-parse --show-toplevel)" && \
  gitnexus analyze > "$TMPDIR/gitnexus-reindex.log" 2>&1 &
) >/dev/null 2>&1
exit 0
EOF
chmod +x .git/hooks/post-commit

⚠ Hooks do NOT copy between git worktrees — re-install per worktree if needed.

Step 4 — Obsidian Wiki structure (Karpathy method)

If {{WIKI_PATH}}\<ProjectName>\wiki\ doesn't exist:

python ~/.claude/skills/dev-wiki/scripts/init_dev_wiki.py --project "<ProjectName>"

Otherwise verify structure:

{{WIKI_PATH}}\<ProjectName>\wiki\
├── index.md          ← Navigation + TOC (<100 lines)
├── SPRINT.md         ← Active sprint (<60 lines)
├── concepts/         ← Cross-cutting patterns
├── sources/          ← Referenced research/docs
├── archive/          ← Completed sprints
└── graph/
    └── knowledge_graph.json   ← Graphify output (L2a)

Premium visual: dev wikis live INSIDE the big {{WIKI_PATH}} vault, which already carries the premium style (gold/dark snippet + project-colored graph) — so a new project subfolder inherits it automatically; do NOT create a nested .obsidian/. ONLY if this project is a standalone vault (its own .obsidian/, e.g. Fakturka.bg / DCTL), style it once:

python ~/.claude/scripts/obsidian_premium_viz.py "{{WIKI_PATH}}\<ProjectName>"

Step 5 — Update project CLAUDE.md (<100 lines)

Add this block near the top:

## 4-Layer Memory (see ~/.claude/references/session-start.md)
- **L4 Pinecone**: `python3 ~/.claude/scripts/pinecone.py query "<ProjectName>" "<q>"`
- **L3 Wiki**: `{{WIKI_PATH}}\<ProjectName>\wiki\`
- **L2b GitNexus**: MCP auto + 7 skills (impact(), pr-review, refactoring, ...)
- **L2a Graphify**: `wiki/graph/knowledge_graph.json` (run `/graphify` if stale)
- **L1**: this CLAUDE.md + `/clear` at 50% context

Step 6 — Graphify JSON (optional, only if project >50 files)

/graphify

Outputs {{WIKI_PATH}}\<ProjectName>\wiki\graph\knowledge_graph.json.

Step 7 — Save initial project summary to Pinecone

python3 ~/.claude/scripts/pinecone.py save "<ProjectName>" \
  "onboarding-$(date +%Y-%m-%d)" \
  "<ProjectName> onboarded to 4-layer memory architecture on $(date +%Y-%m-%d). Stack: <tech-stack>. Main purpose: <one-sentence>. Wiki at {{WIKI_PATH}}\<ProjectName>\wiki\. GitNexus indexed with N nodes. Pinecone namespace: <ProjectName>." \
  --meta "project=<ProjectName>,type=onboarding,date=$(date +%Y-%m-%d)"

Verification Checklist

After Step 7, run these and expect all green:

# 1. GitNexus fresh
cd "{{CODE_PATH}}\<ProjectName>" && gitnexus status | grep -q "up-to-date" && echo "✓ L2b"

# 2. Post-commit hook active
test -x .git/hooks/post-commit && echo "✓ hook"

# 3. Wiki structure
test -f "{{WIKI_PATH}}\<ProjectName>\wiki\index.md" && echo "✓ L3"

# 4. Graphify JSON (if Step 6 done)
test -f "{{WIKI_PATH}}\<ProjectName>\wiki\graph\knowledge_graph.json" && echo "✓ L2a"

# 5. Pinecone writable
python3 ~/.claude/scripts/pinecone.py query "<ProjectName>" "onboarding" --topk 1 | grep -q "onboarding" && echo "✓ L4"

# 6. CLAUDE.md updated
grep -q "4-Layer Memory" "{{CODE_PATH}}\<ProjectName>\CLAUDE.md" && echo "✓ L1"

Output Template (report to user)

✅ <ProjectName> onboarded to 4-layer architecture

| Layer | Status |
|-------|--------|
| L1 CLAUDE.md | updated with 4-layer block |
| L2a Graphify | <fresh/deferred> |
| L2b GitNexus | <N> nodes, <M> edges, ✅ fresh |
| L3 Wiki | {{WIKI_PATH}}\<ProjectName>\wiki\ |
| L4 Pinecone | namespace "<ProjectName>", onboarding saved |

Next sessions will start at ~5k tokens instead of 400k+.
To continue: "Recall last <ProjectName> session"
→ will trigger pinecone.py query + wiki/SPRINT.md read.

---

Initial Global Setup (one-time, if prerequisites missing)

Install GitNexus globally

# On Windows with npm 11.x bug (Cannot destructure property 'package'):
Remove-Item -Recurse -Force "$env:LOCALAPPDATA\npm-cache\_npx"
npm cache clean --force
npm install -g gitnexus
gitnexus setup    # auto-configs Claude Code MCP + 7 skills + PreToolUse/PostToolUse hooks

Pinecone credentials

1. Get API key from https://pinecone.io (free tier)
2. Create index named memory with:
   • dim: 1024
   • metric: cosine
   • model: multilingual-e5-large
3. Save to ~/.claude/.env:

PINECONE_API_KEY=pcsk_xxxxx
PINECONE_INDEX_HOST=memory-<hash>.svc.<region>.pinecone.io
PINECONE_INDEX_NAME=memory
PINECONE_EMBED_MODEL=multilingual-e5-large
PINECONE_DIMENSION=1024

4. chmod 600 ~/.claude/.env
5. Verify:

python3 ~/.claude/scripts/pinecone.py query "test" "hello" --topk 1

Pinecone CLI wrapper

Already at ~/.claude/scripts/pinecone.py — if missing, regenerate via:

Tell Claude: "Re-create pinecone.py CLI wrapper at ~/.claude/scripts/"

Wrapper auto-loads ~/.claude/.env, supports save | query | list | delete per namespace.

~/.claude/.gitignore

Ensure contains .env and *.key so credentials never leak.

---

Token Savings — Expected Impact

Workflow	Before	After	Savings
Session startup	30–50k tokens	~5k	10x
Refactor impact analysis	20k+ grep tokens	~500 (gitnexus impact)	40x
Cross-session recall	re-read history	~300 (pinecone query)	∞
Codebase overview new session	50k+ reads	~2.6k (Graphify JSON)	20x
Typical active session total	500k–1M	~25k	~40x

---

Supported Projects (one-time onboarding required)

Each project gets its own Pinecone namespace, wiki folder, and gitnexus index:

{{CODE_PATH}}\Facturka.bg          → namespace: "Fakturka.bg"      ✅ onboarded 2026-04-17
{{CODE_PATH}}\StroyOffice-Pro      → namespace: "StroyOffice"      ⚪ pending
{{CODE_PATH}}\Higgsfield           → namespace: "Higgsfield"       ⚪ pending
{{CODE_PATH}}\Cinemind             → namespace: "Cinemind"         ⚪ pending
{{CODE_PATH}}\CasinoScore-AI       → namespace: "CasinoScore"      ⚪ pending
...

Run this skill once per project; then just use the normal session-start protocol.