graph/README.md

# Knowledge Graph Artifacts

This directory ships the pre-built ctx LLM-wiki and knowledge graph.

Current snapshot:

- **102,720 graph nodes**
- **2,911,575 graph edges**
- **52 Louvain communities**
- **91,450 skill entity pages** with hydrated installable bodies
- **467 agent pages**
- **10,787 MCP server pages**
- **16 harness pages**
- **89,465 hydrated `SKILL.md` bodies**
- **28,612 long skill bodies converted through the micro-skill gate**

The runtime recommendation paths use this graph in two ways:

- Development recommendations return skills, agents, and MCP servers only.
- Custom/API/local model onboarding recommends harnesses using the higher harness fit floor in `src/config.json`.

## Files

| File | Contents |
|---|---|
| `wiki-graph-runtime.tar.gz` | Fast install artifact used by default `ctx-init --graph`: `graphify-out/*`, the skill index, 16 harness pages, wiki index files, and Obsidian metadata needed for recommendations and harness dry-runs without expanding every entity page |
| `wiki-graph.tar.gz` | Full LLM-wiki: entity pages, converted skill bodies, mirrored agent bodies, concept pages, `graphify-out/graph.json`, `graph-delta.json`, export manifest, communities, skill indexes, and Obsidian metadata |
| Skill catalog gzip | Compressed skill index for the 89,465 body-backed skill entries shipped in the wiki |
| `communities.json` | Current Louvain community export |
| `graphify-out/dashboard-neighborhoods.sqlite3` inside both tarballs | Compact top-neighbor index used by `ctx-monitor` so `/api/graph/<slug>.json` does not cold-parse the 604 MB NetworkX graph |
| `viz-overview.html` | Plotly overview of the graph |
| `viz-python.html` | Python-focused graph view |
| `viz-security.html` | Security-focused graph view |
| `viz-ai-agents.html` | AI-agent-focused graph view |
| `sample-top60.html` | Interactive top-degree sample |

Preview HTML files are generated from the shipped `graphify-out/graph.json`
and embed the graph export ID in `<meta name="ctx-graph-export-id">`. Static
PNG snapshots are intentionally not shipped because they can drift from the
current tarball without an executable freshness check.

## Runtime vs Full Wiki

`ctx-init --graph` installs `wiki-graph-runtime.tar.gz` by default. That is the
right path for recommendations and first-time installs because it avoids
expanding hundreds of thousands of markdown files while still shipping the
harness pages needed by `ctx-harness-install --dry-run`. Use
`ctx-init --graph --graph-install-mode full` or manual full extraction when you
want local wiki browsing, Obsidian, or the converted skill body tree.

## What Is Inside `wiki-graph.tar.gz`

- `entities/skills/` - all skill entity pages
- `entities/agents/` - agent entity pages
- `entities/mcp-servers/<shard>/` - sharded MCP server entity pages
- `entities/harnesses/` - harness entity pages
- `converted/` - installable skill bodies
- `converted-agents/` - mirrored agent bodies
- `concepts/` - community concept pages
- `external-catalogs/` - machine-readable skill index, summary, and coverage metadata
- `graphify-out/graph.json` - NetworkX node-link graph
- `graphify-out/graph-delta.json` - delta export for the latest graph generation
- `graphify-out/graph-export-manifest.json` - export manifest tying graph, delta, communities, and report to one generation
- `graphify-out/communities.json` - community export
- `SCHEMA.md`, `index.md`, `log.md`, `catalog.md` - wiki contract and indexes
- `.obsidian/` - vault metadata for local graph browsing

`SKILL.md.original` backups, transient `.lock` files, and `.ctx/` queue state
are not shipped. Local micro-skill conversion may keep `.original` files for
traceability, but the packaged tarball excludes them so users do not ingest raw
long bodies after conversion.

## Extract

Default runtime install:

```bash
ctx-init --graph
```

Full wiki extraction:

```bash
mkdir -p ~/.claude/skill-wiki
tar xzf graph/wiki-graph.tar.gz -C ~/.claude/skill-wiki/
```

On Windows PowerShell, use the built-in `tar.exe` without `--force-local`:

```powershell
New-Item -ItemType Directory -Force "$env:USERPROFILE\.claude\skill-wiki"
tar -xzf graph\wiki-graph.tar.gz -C "$env:USERPROFILE\.claude\skill-wiki"
```

With Git Bash or MSYS tar, use `--force-local` only when the `-C` target is a
drive-letter path:

```bash
tar --force-local xzf graph/wiki-graph.tar.gz -C C:/Users/<you>/.claude/skill-wiki/
```

## Validate

```bash
python src/validate_graph_artifacts.py --deep
python src/update_repo_stats.py --check
```

For release-count validation, pin the exact snapshot numbers:

```bash
python src/validate_graph_artifacts.py --deep \
  --expected-nodes 102720 \
  --expected-edges 2911575 \
  --expected-semantic-edges 1683163 \
  --expected-harness-nodes 16 \
  --expected-skill-pages 91450 \
  --expected-agent-pages 467 \
  --expected-mcp-pages 10787 \
  --expected-harness-pages 16
```

Manual sanity checks:

```bash
tar -tzf graph/wiki-graph.tar.gz | grep 'graphify-out/graph.json'
tar -tzf graph/wiki-graph.tar.gz | grep 'external-catalogs/.*/catalog.json'
tar -tzf graph/wiki-graph.tar.gz | grep 'SKILL.md.original' && exit 1 || true
tar -tzf graph/wiki-graph.tar.gz | grep '\.lock$' && exit 1 || true
tar -tzf graph/wiki-graph.tar.gz | grep '^\./\.ctx/' && exit 1 || true
```

Windows PowerShell equivalent for the exclusion checks:

```powershell
tar -tzf graph/wiki-graph.tar.gz | Select-String 'SKILL.md.original'
tar -tzf graph/wiki-graph.tar.gz | Select-String '\.lock$'
tar -tzf graph/wiki-graph.tar.gz | Select-String '^\./\.ctx/'
```

The PowerShell commands should print nothing.

## Rebuild

After adding or updating skills, agents, MCP servers, or harnesses:

```bash
ctx-wiki-worker --wiki ~/.claude/skill-wiki --limit 1
ctx-scan-repo --repo . --recommend
```

The worker path is the fast local update path. It validates the queued entity
page, updates the wiki index, and attempts incremental ANN attach into
`graphify-out/entity-overlays.jsonl` when the semantic vector index exists. It
also queues the normal incremental graph export job, so a full rebuild remains
the reconciliation path for release artifacts.

If the worker reports that incremental attach was skipped because no vector
index exists, build the exact portable index:

```bash
ctx-wiki-graphify \
  --wiki-dir ~/.claude/skill-wiki \
  --incremental \
  --graph-only \
  --semantic-vector-index numpy-flat
```

Then drain pending queue work again:

```bash
ctx-wiki-worker --wiki ~/.claude/skill-wiki
```

Before promoting an ANN backend or changed thresholds, run the shadow gate:

```bash
ctx-incremental-shadow \
  --index-dir ~/.claude/skill-wiki/.embedding-cache/graph/vector-index \
  --graph ~/.claude/skill-wiki/graphify-out/graph.json \
  --sample-size 100 \
  --min-overlap 0.85
```

It reports precision/recall, top-k agreement, score deltas, and bad examples;
the release gate fails when recall at the largest requested top-k is below the
overlap floor.

For release artifact rebuilds:

```bash
python scripts/graph_artifact_guard.py park
ctx-wiki-graphify
python src/validate_graph_artifacts.py --deep
python src/update_repo_stats.py --check
```

`park` sets Git's local `skip-worktree` bit for the heavyweight generated
archives: `graph/wiki-graph.tar.gz`, `graph/wiki-graph-runtime.tar.gz`, and
the compressed skill index. Keep them parked while graph/wiki generation,
validation, dashboard smoke, and stats checks are still in progress. This
prevents background Git integrations from repeatedly staging hundreds of
megabytes through the Git LFS clean filter. When the release candidate is final,
unpark and stage the artifacts exactly once:

```bash
python scripts/graph_artifact_guard.py unpark
git add graph/wiki-graph.tar.gz graph/wiki-graph-runtime.tar.gz graph/*.json.gz
python scripts/graph_artifact_guard.py prune
```

If a local Git integration gets interrupted while artifacts are dirty,
`python scripts/graph_artifact_guard.py prune` removes unreachable local Git
objects and prunable local LFS cache entries. It does not delete tracked graph
files, rewrite history, or change the remote LFS store.

For a bulk skill refresh, update the existing shipped tarball through the
release refresh path:

```bash
python src/import_skills_sh_catalog.py \
  --from-catalog <skill-catalog.json.gz> \
  --catalog-out <skill-catalog.json.gz> \
  --wiki-tar graph/wiki-graph.tar.gz \
  --update-wiki-tar
```

For a full local wiki repack, write the tarball to the sibling staged path,
then promote that staged candidate after validation:

```bash
cd ~/.claude/skill-wiki
tar --force-local -czf /path/to/ctx/graph/wiki-graph.tar.gz.staged \
    --exclude='.trash' \
    --exclude='__pycache__' \
    --exclude='./raw' \
    --exclude='./.embedding-cache' \
    --exclude='./.ingest-checkpoint' \
    --exclude='./.enrich-checkpoint' \
    --exclude='./.ctx' \
    --exclude='./graphify-out/graph.pickle' \
    --exclude='*.original' \
    --exclude='*.lock' \
    .
cd /path/to/ctx
python -c "from pathlib import Path; from ctx.core.wiki.artifact_promotion import promote_staged_artifact; from import_skills_sh_catalog import _validate_wiki_tarball_candidate; promote_staged_artifact(Path('graph/wiki-graph.tar.gz.staged'), Path('graph/wiki-graph.tar.gz'), validate=_validate_wiki_tarball_candidate)"
```

The repack command above is for Git Bash/MSYS. In Linux/macOS shells omit
`--force-local`; in PowerShell use `tar -czf` without `--force-local`.

Both flows validate candidates before atomic promotion. Each promoted artifact
gets a sibling `*.promotion.json` file with current, candidate, and `last_good`
hashes for review or rollback. The graph, delta, communities, report, and
export manifest are shipped together and carry the same export ID so validation
can reject mixed or partially refreshed graph generations. Raw `.original`
backups, transient `.lock` files, and `.ctx/` queue state must not appear in
the shipped tarball.

## Implementation Notes

The graph is built by `ctx.core.wiki.wiki_graphify` and the `ctx-wiki-graphify`
console script. Edges blend semantic similarity, explicit tag overlap,
slug-token overlap, source overlap, direct links, quality, usage, type affinity,
and graph-structure signals where available. The shipped default
`graph.min_edge_weight` is `0.03`, chosen from artifact calibration because it
keeps the current topology intact while recording the real shipped floor.

`nashsu/llm_wiki` was reviewed for design ideas around persistent wiki
contracts, queues, retrieval, and graph maintenance. ctx does not vendor that
code in this MIT repository.