memex/docs/SETUP.md

# Setup Guide

Complete installation for the full automation pipeline. For the conceptual
version (just the idea, no scripts), see the "Quick start — Path A" section
in the [README](../README.md).

Tested on macOS (work machines) and Linux/WSL2 (home machines). Should work
on any POSIX system with Python 3.11+, Node.js 18+, and bash.

---

## 1. Prerequisites

### Required

- **git** with SSH or HTTPS access to your remote (for cross-machine sync)
- **Node.js 18+** (for `qmd` search)
- **Python 3.11+** (for all pipeline scripts)
- **`claude` CLI** with valid authentication — Max subscription OAuth or
  API key. Required for summarization and the harvester's AI compile step.
  Without `claude`, you can still use the wiki, but the automation layer
  falls back to manual or local-LLM paths.

### Python tools (recommended via `pipx`)

```bash
# URL content extraction — required for wiki-harvest.py
pipx install trafilatura
pipx install crawl4ai && crawl4ai-setup    # installs Playwright browsers
```

Verify: `trafilatura --version` and `crwl --help` should both work.

### Optional

- **`pytest`** — only needed to run the test suite (`pip install --user pytest`)
- **`llama.cpp` / `llama-server`** — only if you want the legacy local-LLM
  summarization path instead of `claude -p`

---

## 2. Clone the repo

```bash
git clone <your-gitea-or-github-url> ~/projects/wiki
cd ~/projects/wiki
```

The repo contains scripts, tests, docs, and example content — but no
actual wiki pages. The wiki grows as you use it.

---

## 3. Configure qmd search

`qmd` handles BM25 full-text search and vector search over the wiki.
The pipeline uses **three** collections:

- **`wiki`** — live content (patterns/decisions/concepts/environments),
  staging, and raw sources. The default search surface.
- **`wiki-archive`** — stale / superseded pages. Excluded from default
  search; query explicitly with `-c wiki-archive` when digging into
  history.
- **`wiki-conversations`** — mined Claude Code session transcripts.
  Excluded from default search because they'd flood results with noisy
  tool-call output; query explicitly with `-c wiki-conversations` when
  looking for "what did I discuss about X last month?"

```bash
npm install -g @tobilu/qmd
```

Configure via YAML directly — the CLI doesn't support `ignore` or
`includeByDefault`, so we edit the config file:

```bash
mkdir -p ~/.config/qmd
cat > ~/.config/qmd/index.yml <<'YAML'
collections:
  wiki:
    path: /Users/YOUR_USER/projects/wiki   # ← replace with your actual path
    pattern: "**/*.md"
    ignore:
      - "archive/**"
      - "reports/**"
      - "plans/**"
      - "conversations/**"
      - "scripts/**"
      - "context/**"

  wiki-archive:
    path: /Users/YOUR_USER/projects/wiki/archive
    pattern: "**/*.md"
    includeByDefault: false

  wiki-conversations:
    path: /Users/YOUR_USER/projects/wiki/conversations
    pattern: "**/*.md"
    includeByDefault: false
    ignore:
      - "index.md"
YAML
```

On Linux/WSL, replace `/Users/YOUR_USER` with `/home/YOUR_USER`.

Build the indexes:

```bash
qmd update     # scan files into all three collections
qmd embed      # generate vector embeddings (~2 min first run + ~30 min for conversations on CPU)
```

Verify:

```bash
qmd collection list
# Expected:
#   wiki                — N files
#   wiki-archive        — M files [excluded]
#   wiki-conversations  — K files [excluded]
```

The `[excluded]` tag on the non-default collections confirms
`includeByDefault: false` is honored.

**When to query which**:

```bash
# "What's the current pattern for X?"
qmd search "topic" --json -n 5

# "What was the OLD pattern, before we changed it?"
qmd search "topic" -c wiki-archive --json -n 5

# "When did we discuss this, and what did we decide?"
qmd search "topic" -c wiki-conversations --json -n 5

# Everything — history + current + conversations
qmd search "topic" -c wiki -c wiki-archive -c wiki-conversations --json -n 10
```

---

## 4. Configure the Python scripts

Three scripts need per-user configuration:

### `scripts/extract-sessions.py` — `PROJECT_MAP`

This maps Claude Code project directory suffixes to short wiki codes
("wings"). Claude stores sessions under `~/.claude/projects/<hashed-path>/`
where the hashed path is derived from the absolute path to your project.

Open the script and edit the `PROJECT_MAP` dict near the top. Look for
the `CONFIGURE ME` block. Examples:

```python
PROJECT_MAP: dict[str, str] = {
    "projects-wiki": "wiki",
    "-claude": "cl",
    "my-webapp": "web",       # map "mydir/my-webapp" → wing "web"
    "mobile-app": "mob",
    "work-monorepo": "work",
    "-home": "general",       # catch-all for unmatched sessions
}
```

Run `ls ~/.claude/projects/` to see what directory names Claude is
actually producing on your machine — the suffix in `PROJECT_MAP` matches
against the end of each directory name.

### `scripts/update-conversation-index.py` — `PROJECT_NAMES` / `PROJECT_ORDER`

Matching display names for every code in `PROJECT_MAP`:

```python
PROJECT_NAMES: dict[str, str] = {
    "wiki": "WIKI — This Wiki",
    "cl": "CL — Claude Config",
    "web": "WEB — My Webapp",
    "mob": "MOB — Mobile App",
    "work": "WORK — Day Job",
    "general": "General — Cross-Project",
}

PROJECT_ORDER = [
    "work", "web", "mob",   # most-active first
    "wiki", "cl", "general",
]
```

### `scripts/wiki-harvest.py` — `SKIP_DOMAIN_PATTERNS`

Add your internal/personal domains so the harvester doesn't try to fetch
them. Patterns use `re.search`:

```python
SKIP_DOMAIN_PATTERNS = [
    # ... (generic ones are already there)
    r"\.mycompany\.com$",
    r"^git\.mydomain\.com$",
]
```

---

## 5. Create the post-merge hook

The hook rebuilds the qmd index automatically after every `git pull`:

```bash
cat > ~/projects/wiki/.git/hooks/post-merge <<'HOOK'
#!/usr/bin/env bash
set -euo pipefail

if command -v qmd &>/dev/null; then
  echo "wiki: rebuilding qmd index..."
  qmd update 2>/dev/null
  # WSL / Linux: no GPU, force CPU-only embeddings
  if [[ "$(uname -s)" == "Linux" ]]; then
    NODE_LLAMA_CPP_GPU=false qmd embed 2>/dev/null
  else
    qmd embed 2>/dev/null
  fi
  echo "wiki: qmd index updated"
fi
HOOK
chmod +x ~/projects/wiki/.git/hooks/post-merge
```

`.git/hooks/` isn't tracked by git, so this step runs on every machine
where you clone the repo.

---

## 6. Backfill frontmatter (first-time setup or fresh clone)

If you're starting with existing wiki pages that don't yet have
`last_verified` or `origin`, backfill them:

```bash
cd ~/projects/wiki

# Backfill last_verified from last_compiled/git/mtime
python3 scripts/wiki-hygiene.py --backfill

# Backfill origin: manual on pre-automation pages (one-shot inline)
python3 -c "
import sys
sys.path.insert(0, 'scripts')
from wiki_lib import iter_live_pages, write_page
changed = 0
for p in iter_live_pages():
    if 'origin' not in p.frontmatter:
        p.frontmatter['origin'] = 'manual'
        write_page(p)
        changed += 1
print(f'{changed} page(s) backfilled')
"
```

For a brand-new empty wiki, there's nothing to backfill — skip this step.

---

## 7. Run the pipeline manually once

Before setting up cron, do a full end-to-end dry run to make sure
everything's wired up:

```bash
cd ~/projects/wiki

# 1. Extract any existing Claude Code sessions
bash scripts/mine-conversations.sh --extract-only

# 2. Summarize with claude -p (will make real LLM calls — can take minutes)
python3 scripts/summarize-conversations.py --claude

# 3. Regenerate conversation index + wake-up context
python3 scripts/update-conversation-index.py --reindex

# 4. Dry-run the maintenance pipeline
bash scripts/wiki-maintain.sh --dry-run --no-compile
```

Expected output from step 4: all three phases run, phase 3 (qmd reindex)
shows as skipped in dry-run mode, and you see `finished in Ns`.

---

## 8. Cron setup (optional)

If you want full automation, add these cron jobs. **Run them on only ONE
machine** — state files sync via git, so the other machine picks up the
results automatically.

```bash
crontab -e
```

```cron
# Wiki SSH key for cron (if your remote uses SSH with a key)
GIT_SSH_COMMAND="ssh -i /path/to/wiki-key -o StrictHostKeyChecking=no"

# PATH for cron so claude, qmd, node, python3, pipx tools are findable
PATH=/home/YOUR_USER/.nvm/versions/node/v22/bin:/home/YOUR_USER/.local/bin:/usr/local/bin:/usr/bin:/bin

# ─── Sync ──────────────────────────────────────────────────────────────────
# commit/pull/push every 15 minutes
*/15 * * * * /home/YOUR_USER/projects/wiki/scripts/wiki-sync.sh --commit && /home/YOUR_USER/projects/wiki/scripts/wiki-sync.sh --pull && /home/YOUR_USER/projects/wiki/scripts/wiki-sync.sh --push >> /tmp/wiki-sync.log 2>&1

# full sync with qmd reindex every 2 hours
0 */2 * * * /home/YOUR_USER/projects/wiki/scripts/wiki-sync.sh full >> /tmp/wiki-sync.log 2>&1

# ─── Mining ────────────────────────────────────────────────────────────────
# Extract new sessions hourly (no LLM, fast)
0 * * * * /home/YOUR_USER/projects/wiki/scripts/mine-conversations.sh --extract-only >> /tmp/wiki-mine.log 2>&1

# Summarize + index daily at 2am (uses claude -p)
0 2 * * * cd /home/YOUR_USER/projects/wiki && python3 scripts/summarize-conversations.py --claude >> /tmp/wiki-mine.log 2>&1 && python3 scripts/update-conversation-index.py --reindex >> /tmp/wiki-mine.log 2>&1

# ─── Maintenance ───────────────────────────────────────────────────────────
# Daily at 3am: harvest + quick hygiene + qmd reindex
0 3 * * * cd /home/YOUR_USER/projects/wiki && bash scripts/wiki-maintain.sh >> scripts/.maintain.log 2>&1

# Weekly Sunday at 4am: full hygiene with LLM checks
0 4 * * 0 cd /home/YOUR_USER/projects/wiki && bash scripts/wiki-maintain.sh --hygiene-only --full >> scripts/.maintain.log 2>&1
```

Replace `YOUR_USER` and the node path as appropriate for your system.

**macOS note**: `cron` needs Full Disk Access if you're pointing it at
files in `~/Documents` or `~/Desktop`. Alternatively use `launchd` with
a plist — same effect, easier permission model on macOS.

**WSL note**: make sure `cron` is actually running (`sudo service cron
start`). Cron doesn't auto-start in WSL by default.

**`claude -p` in cron**: OAuth tokens must be cached before cron runs it.
Run `claude --version` once interactively as your user to prime the
token cache — cron then picks up the cached credentials.

---

## 9. Tell Claude Code about the wiki

Two separate CLAUDE.md files work together:

1. **The wiki's own `CLAUDE.md`** at `~/projects/wiki/CLAUDE.md` — the
   schema the agent reads when working INSIDE the wiki. Tells it how to
   maintain pages, apply frontmatter, handle staging/archival.
2. **Your global `~/.claude/CLAUDE.md`** — the user-level instructions
   the agent reads on EVERY session (regardless of directory). Tells it
   when and how to consult the wiki from any other project.

Both are provided as starter templates you can copy and adapt:

### (a) Wiki schema — copy to the wiki root

```bash
cp ~/projects/wiki/docs/examples/wiki-CLAUDE.md ~/projects/wiki/CLAUDE.md
# then edit ~/projects/wiki/CLAUDE.md for your own conventions
```

This file is ~200 lines. It defines:
- Directory structure and the automated-vs-manual core rule
- Frontmatter spec (required fields, staging fields, archive fields)
- Page-type conventions (pattern / decision / environment / concept)
- Operations: Ingest, Query, Mine, Harvest, Maintain, Lint
- **Search Strategy** — which of the three qmd collections to use for
  which question type

Customize the sections marked **"Customization Notes"** at the bottom
for your own categories, environments, and cross-reference format.

### (b) Global wake-up + query instructions

Append the contents of `docs/examples/global-CLAUDE.md` to your global
Claude Code instructions:

```bash
cat ~/projects/wiki/docs/examples/global-CLAUDE.md >> ~/.claude/CLAUDE.md
# then review ~/.claude/CLAUDE.md to integrate cleanly with any existing
# content
```

This adds:
- **Wake-Up Context** — read `context/wake-up.md` at session start
- **LLM Wiki — When to Consult It** — query mode vs ingest mode rules
- **LLM Wiki — How to Search It** — explicit guidance for all three qmd
  collections (`wiki`, `wiki-archive`, `wiki-conversations`) with
  example queries for each
- **Rules When Citing** — flag `confidence: low`, `status: pending`,
  and archived pages to the user

Together these give the agent a complete picture: how to maintain the
wiki when working inside it, and how to consult it from anywhere else.

---

## 10. Verify

```bash
cd ~/projects/wiki

# Sync state
bash scripts/wiki-sync.sh --status

# Search
qmd collection list
qmd search "test" --json -n 3   # won't return anything if wiki is empty

# Mining
tail -20 scripts/.mine.log 2>/dev/null || echo "(no mining runs yet)"

# End-to-end maintenance dry-run (no writes, no LLM, no network)
bash scripts/wiki-maintain.sh --dry-run --no-compile

# Run the test suite
cd tests && python3 -m pytest
```

Expected:
- `qmd collection list` shows all three collections: `wiki`, `wiki-archive [excluded]`, `wiki-conversations [excluded]`
- `wiki-maintain.sh --dry-run` completes all three phases
- `pytest` passes all 171 tests in ~1.3 seconds

---

## Troubleshooting

**qmd search returns nothing**
```bash
qmd collection list          # verify path points at the right place
qmd update                   # rebuild index
qmd embed                    # rebuild embeddings
cat ~/.config/qmd/index.yml  # verify config is correct for your machine
```

**qmd collection points at the wrong path**
Edit `~/.config/qmd/index.yml` directly. Don't use `qmd collection add`
from inside the target directory — it can interpret the path oddly.

**qmd returns archived pages in default searches**
Verify `wiki-archive` has `includeByDefault: false` in the YAML and
`qmd collection list` shows `[excluded]`.

**`claude -p` fails in cron ("not authenticated")**
Cron has no browser. Run `claude --version` once as the same user
outside cron to cache OAuth tokens; cron will pick them up. Also verify
the `PATH` directive at the top of the crontab includes the directory
containing `claude`.

**`wiki-harvest.py` fetch failures**
```bash
# Verify the extraction tools work
trafilatura -u "https://example.com" --markdown --no-comments --precision
crwl "https://example.com" -o markdown-fit

# Check harvest state
python3 -c "import json; print(json.dumps(json.load(open('.harvest-state.json'))['failed_urls'], indent=2))"
```

**`wiki-hygiene.py` archived a page unexpectedly**
Check `last_verified` vs decay thresholds. If the page was never
referenced in a conversation, it decayed naturally. Restore with:
```bash
python3 scripts/wiki-hygiene.py --restore archive/patterns/foo.md
```

**Both machines ran maintenance simultaneously**
Merge conflicts on `.harvest-state.json` / `.hygiene-state.json` will
occur. Pick ONE machine for maintenance; disable the maintenance cron
on the other. Leave sync cron running on both so changes still propagate.

**Tests fail**
Run `cd tests && python3 -m pytest -v` for verbose output. If the
failure mentions `WIKI_DIR` or module loading, verify
`scripts/wiki_lib.py` exists and contains the `WIKI_DIR` env var override
near the top.

---

## Minimal install (skip everything except the idea)

If you want the conceptual wiki without any of the automation, all you
actually need is:

1. An empty directory
2. `CLAUDE.md` telling your agent the conventions (see the schema in
   [`ARCHITECTURE.md`](ARCHITECTURE.md) or Karpathy's gist)
3. `index.md` for the agent to catalog pages
4. An agent that can read and write files (any Claude Code, Cursor, Aider
   session works)

Then tell the agent: "Start maintaining a wiki here. Every time I share
a source, integrate it. When I ask a question, check the wiki first."

You can bolt on the automation layer later if/when it becomes worth
the setup effort.