| # Knowledge graph | |
| A pre-built weighted graph of skills, agents, MCP servers, and cataloged | |
| harnesses in the ctx ecosystem, shipped as `graph/wiki-graph.tar.gz`. | |
| The on-disk JSON and `resolve_graph` Python API are harness-aware, including | |
| plain-slug graph walks from `harness:<slug>` nodes. `ctx-monitor` | |
| exposes skill/agent/MCP/harness wiki and graph views. Harness installation, | |
| update, and uninstall are handled by `ctx-harness-install`; dashboard | |
| load/unload POSTs deliberately reject harnesses and return the dry-run CLI | |
| command to use instead. Quality scoring is exposed for sidecar-backed skills, | |
| agents, and MCP servers. | |
| ## What's in it | |
| Authoritative numbers from the shipped tarball. The curated-core snapshot | |
| is **13,233 nodes** (1,969 curated skills + 464 agents + 10,787 MCP servers | |
| + 13 harnesses). Harness pages under `entities/harnesses/` are ingested into | |
| local rebuilds and the separate harness-catalog recommendation path. The | |
| tarball also carries **89,463 body-backed Skills.sh `skill` nodes**, | |
| matching skill pages under `entities/skills/skills-sh-*.md`. **89,463** | |
| hydrated Skills.sh bodies are shipped as installable `SKILL.md` files under | |
| `converted/skills-sh-*/`; the **28,612** entries over the configured line | |
| limit were converted to gated micro-skill orchestrators. Full original bodies | |
| are used during graph rebuilds for semantic similarity, but | |
| `SKILL.md.original` backups and transient `.lock` files are omitted from the | |
| shipped tarball. | |
| | | Count | | |
| |---|---:| | |
| | Total nodes | **102,696** | | |
| | Curated core nodes | **13,233** (1,969 skills + 464 agents + 10,787 MCP servers + 13 harnesses) | | |
| | Remote-cataloged Skills.sh skill nodes | **89,463** (`skill`, `status=remote-cataloged`, body-backed) | | |
| | Total edges | **2,900,834** | | |
| | Skills.sh incident edges | **2,605,971** | | |
| | Skills.sh semantic incident edges | **1,500,685** | | |
| | Communities | **52** (Louvain) | | |
| | Edge sources (overlap-deduped) | semantic 1,682,825 - tag 891,684 - token 433,074 | | |
| | Cross-type edges (skill <-> agent) | ~65K | | |
| | Cross-type edges (skill <-> MCP) | ~41K | | |
| | Cross-type edges (agent <-> MCP) | ~223 | | |
| | Harness edges | **3,289** | | |
| | Skills.sh catalog | **89,463** observed body-backed entries (`external-catalogs/skills-sh/catalog.json` + `entities/skills/skills-sh-*.md`) | | |
| ## Install | |
| Extract the tarball into your `~/.claude/skill-wiki/` to get a | |
| ready-to-query graph plus every shipped skill/agent/MCP entity page, | |
| cataloged harness pages when present, remote-cataloged Skills.sh skill | |
| pages, concept pages, and converted micro-skill pipelines. The extracted | |
| tree also includes the Skills.sh catalog JSON used by the shared | |
| recommender: | |
| ```bash | |
| mkdir -p ~/.claude/skill-wiki | |
| tar xzf graph/wiki-graph.tar.gz -C ~/.claude/skill-wiki/ | |
| ``` | |
| On Windows PowerShell, create the target and use the built-in `tar.exe` | |
| without `--force-local`: | |
| ```powershell | |
| New-Item -ItemType Directory -Force "$env:USERPROFILE\.claude\skill-wiki" | Out-Null | |
| tar -xzf graph\wiki-graph.tar.gz -C "$env:USERPROFILE\.claude\skill-wiki" | |
| ``` | |
| The extracted tree also opens directly as an Obsidian vault — the | |
| `.obsidian/` config ships inside the tarball — so you can use | |
| Obsidian's native graph view if you prefer it to the web dashboard. | |
| ## How edges are built | |
| Edges are built and explained by the `ctx-wiki-graphify` console script | |
| (`ctx.core.wiki.wiki_graphify`). A pair must first have at least one base | |
| signal: | |
| 1. **Semantic cosine** — when the embedding backend is available, entity | |
| text is embedded and semantic neighbors above the configured build floor | |
| contribute weighted edges. | |
| 2. **Explicit frontmatter tags** — each entity page's YAML `tags:` | |
| list contributes edges between every pair of entities that share | |
| a tag. Popular tags capped at 500 nodes to avoid noise-floor | |
| "everything connects to everything" mega-buckets like `typescript` | |
| or `frontend`. | |
| 3. **Slug-token pseudo-tags** — each hyphenated slug contributes its | |
| tokens as implicit tags. `fastapi-pro` contributes `fastapi`; | |
| `python-patterns` contributes `python` and `patterns`. A stop-word | |
| filter drops generic tokens like `skill`, `agent`, `pro`, `expert`, | |
| `core` so they don't over-connect the graph. | |
| 4. **Source overlap** — pages with the same high-specificity source URL, | |
| repository URL, homepage, detail URL, or package URL can connect even | |
| when their tags differ. Dense source buckets are skipped. | |
| 5. **Direct wikilinks** — explicit entity links such as | |
| `[[entities/agents/code-reviewer]]` create a direct graph edge. | |
| Edge `weight` is the final blended strength. Semantic, tag, and token | |
| weights form the base blend from `config.json`; source overlap and direct | |
| links add configured boosts. Existing edges can also receive explainable | |
| ranking boosts from Adamic-Adar shared-neighbor structure, type affinity, | |
| usage telemetry, and quality scores. Those boost-only signals do not create | |
| edges by themselves. The shipped default `graph.min_edge_weight` is `0.03`; | |
| calibration against the 2026-05 shipped graph showed this is the highest | |
| floor with zero edge loss, while `0.05` would remove roughly 29.7% of edges. | |
| Edge metadata keeps the ingredients explainable: `semantic_sim`, | |
| `shared_tags`, `shared_tokens`, `shared_sources`, `direct_link`, | |
| `adamic_adar`, `type_affinity`, `usage_score`, `quality_score`, | |
| `edge_reasons`, and `score_components`. Hydrated Skills.sh records use their | |
| full source bodies during graph rebuilds, so long converted entries keep | |
| full-body similarity even though the shipped installable `SKILL.md` files are | |
| short gated loaders. The raw `SKILL.md.original` backups are build inputs, not | |
| tarball members. | |
| ## Communities | |
| After edges are built, `wiki_graphify` runs NetworkX's Louvain | |
| community detection (`resolution=1.2`, `seed=42` for determinism). | |
| The result is **52 communities** ranging from single-member isolated | |
| specialists to several thousand members in broad clusters like | |
| `Community + Official + AI`. Each community also gets an auto-generated | |
| `concepts/<community>.md` wiki page summarizing its members and top | |
| shared tags. | |
| The legacy CNM ("greedy modularity") algorithm is still available | |
| behind `CTX_GRAPH_COMMUNITY=cnm` — it's deterministic but O(n²) on | |
| dense graphs and hangs on the live 13K-node dataset (~50min run was | |
| killed on 2026-04-27 inside the priority-queue siftup). Louvain is | |
| the default because it finishes in seconds and produces equivalent | |
| quality clusters for the recommendation use case. | |
| ## Querying the graph | |
| ### Via the dashboard | |
| ```bash | |
| ctx-monitor serve # http://127.0.0.1:8765 | |
| ``` | |
| Then open `/graph?slug=<entity-slug>&type=<entity-type>` for a | |
| cytoscape neighborhood view, or | |
| `/api/graph/<slug>.json?type=<entity-type>&hops=1&limit=40` for the | |
| dashboard-shaped JSON. The `type` query is optional for unique slugs and | |
| recommended for duplicate slugs such as `langgraph`. See the | |
| [dashboard reference](dashboard.md) for the full route catalogue. | |
| ### Via Python | |
| ```python | |
| import json | |
| from pathlib import Path | |
| from networkx.readwrite import node_link_graph | |
| raw = json.loads( | |
| Path("~/.claude/skill-wiki/graphify-out/graph.json").expanduser().read_text() | |
| ) | |
| edges_key = "links" if "links" in raw else "edges" | |
| G = node_link_graph(raw, edges=edges_key) | |
| # 102,696 nodes, 2,900,834 edges | |
| print(G.number_of_nodes(), G.number_of_edges()) | |
| # Find entities related to 'fastapi-pro' by edge weight | |
| seed = "skill:fastapi-pro" | |
| neighbors = sorted( | |
| G.neighbors(seed), | |
| key=lambda n: G[seed][n]["weight"], | |
| reverse=True, | |
| )[:10] | |
| for n in neighbors: | |
| shared = G[seed][n].get("shared_tags", []) | |
| print(f" w={G[seed][n]['weight']:>2} {G.nodes[n]['label']:<40} {shared[:3]}") | |
| ``` | |
| The node-link JSON schema's edges key is auto-detected (legacy | |
| NetworkX 2.x used `"links"`; current versions default to `"edges"`). | |
| The helper `resolve_graph.load_graph()` does this for you. | |
| ### Via recommendation paths | |
| The graph backs two recommendation paths: | |
| - Execution recommendation surfaces (`ctx.recommend_bundle`, MCP | |
| `ctx__recommend_bundle`, generic harness tools, Claude Code hook | |
| suggestions, and repo-scan advisory output) share | |
| `ctx.core.resolve.recommendations.recommend_by_tags` for skills, | |
| agents, and MCP servers. That engine ranks candidates by | |
| slug-token matches, tag overlap, graph degree, and semantic-cache | |
| signals when available. Skills.sh results are `skill` nodes with | |
| `source_catalog=skills.sh`, `detail_url`, `install_command`, duplicate | |
| hints, gated micro-skill loaders when over the line threshold, and | |
| quality/security metadata. If an older | |
| extracted wiki has the Skills.sh catalog JSON but no graph nodes for | |
| those records, the same recommender falls back to the catalog file. | |
| - Harness recommendations are a separate catalog path for custom/API/local | |
| model onboarding (`ctx-init --model-mode custom ...`) and | |
| `ctx-harness-install`. They use the same graph catalog filtered to | |
| `harness` nodes and the higher harness match floor from `config.json`. | |
| - Repository scans still start from stack detections, then turn that profile | |
| into the same tag/query bundle used by the execution recommender. If a | |
| shipped graph is unavailable, scan output falls back to the legacy installed | |
| skill resolver so a plain profile scan remains useful. Harnesses are | |
| intentionally not emitted from repo scans or Claude Code hook bundles. | |
| This split is intentional: execution surfaces need identical ranking and a | |
| small top-K, while harness choice changes the model runtime itself and belongs | |
| in an explicit onboarding/install flow. | |
| ### LLM-wiki design references | |
| ctx follows Karpathy's LLM-wiki pattern. We also reviewed | |
| [`nashsu/llm_wiki`](https://github.com/nashsu/llm_wiki) as a design reference | |
| for source traceability, persistent ingest queues, graph insights, and | |
| budgeted token/vector/graph retrieval. That repository is GPLv3, while ctx is | |
| MIT, so ctx can use those ideas as product inspiration but must not copy or | |
| vendor its code or assets. | |
| ## Rebuilding | |
| After you add a skill, agent, MCP server, or harness entity page: | |
| ```bash | |
| ctx-wiki-graphify # rebuild entity graph + communities | |
| ``` | |
| The pre-commit hook (`.githooks/pre-commit`) does **not** rebuild or | |
| repack graph artifacts from `~/.claude/skill-wiki/`; that local wiki can | |
| contain private entities. It refreshes cheap README stats when relevant | |
| checked-in files are staged and warns when entity sources changed. Run | |
| `ctx-wiki-graphify`, validate, repack, and stage the artifacts explicitly | |
| for skill, agent, MCP server, or harness catalog releases. | |
| Graphify exports stage and validate each generated artifact before atomic | |
| promotion. `graph.json`, `graph-delta.json`, `communities.json`, | |
| `graph-report.md`, and `graph-export-manifest.json` each get a sibling | |
| `*.promotion.json` file with candidate, current, and `last_good` hashes plus | |
| rollback metadata. The manifest is promoted last, so a crash between artifact | |
| promotion and manifest promotion is detected as an incomplete export and the | |
| next run rebuilds instead of trusting mixed graph files. | |
| ## Edge-count history | |
| | Version | Edges | Note | | |
| |---|---|---| | |
| | v0.5.x | 642K (stale) / 861 (live) | Bundle had stale 642K; live rebuild silently produced 861 because `DENSE_TAG_THRESHOLD=20` dropped every popular tag. | | |
| | v0.6.0 | 454,719 | Threshold raised to 500, multi-line YAML lists parsed, slug-token pseudo-tags added. | | |
| | v0.7.x | 847,207 | Pulsemcp ingest added 10,786 MCP server nodes; sentence-embedding semantic edges added. | | |
| | 2026-04-27 graph rebuild pass | **963,068** | +21 mattpocock skills, +156 designdotmd designs (+106,702 edges); patch-path bug fixed (graphify now forces full rebuild when prior graph has 0 semantic edges but current run computed semantic pairs); community detection switched from CNM to Louvain. | | |
| | 2026-04-29 Skills.sh remote-cataloged pass | **1,030,831** | +90,846 first-class `skill` nodes, +90,846 skill pages, and +67,519 sparse duplicate/tag metadata edges to the curated graph. Full-body semantic edges are intentionally deferred to the hydration pass. | | |
| | 2026-04-29 text-to-cad harness pass | **1,031,011** | +1 first-class `harness` node, +1 harness page, and +224 explainable harness edges, including 44 remote-cataloged Skills.sh edges. | | |
| | 2026-04-29 curated harness catalog pass | **1,033,253** | +12 first-class `harness` nodes/pages for LangGraph, CrewAI, AutoGen, Google ADK, Semantic Kernel, Mastra, Pydantic AI, Haystack, OpenAI Agents SDK, LiteLLM, Langfuse, and AgentOps; harness incident edges now total 2,700. | | |
| | 2026-04-30 Skills.sh semantic hydration pass | **2,881,027** | +full-body semantic edges for hydrated Skills.sh records; semantic top-K became the dominant large-scale signal. | | |
| | 2026-05-01 Skills.sh micro-skill pass | **2,960,189** | Enforced the <=180-line loader threshold across 89,461 hydrated Skills.sh `SKILL.md` files, converted 28,611 long bodies into gated micro-skill orchestrators, used full originals for semantic graphing, excluded `.original` backups from the shipped tarball, bounded generated stage/reference files to 40 lines, and rebuilt the graph. | | |
| | 2026-05-02 GitNexus MCP pass | **2,960,215** | Added GitNexus as a cataloged MCP server entity with 26 cross-type edges to its Skills.sh skill pages and related architecture/refactoring agents; semantic edge count unchanged. | | |
| | 2026-05-04 v0.7.3 artifact refresh | **2,960,215** | Hydrated one recoverable Skills.sh command-injection-testing body, raising hydrated Skills.sh `SKILL.md` files to 89,463; generated micro-skill markdown now defangs high-risk command-injection payloads before packaging. Graph topology unchanged. | | |
| | 2026-05-04 body-backed Skills.sh prune | **2,900,834** | Removed 1,383 Skills.sh records that had no packaged `SKILL.md` body and no parseable Skills.sh prose body. Remaining Skills.sh catalog entries, graph nodes, entity pages, and converted `SKILL.md` bodies are all **89,463**. | | |
| | 2026-05-05 artifact hygiene refresh | **2,900,834** | Repacked `graph/wiki-graph.tar.gz` to remove transient `.lock` files from the shipped LLM-wiki. Topology unchanged; current tar members: **598,135**. | | |
| The full audit history lives in `CHANGELOG.md`. The current build is | |
| fully reproducible from the wiki content. | |
| ## Pre-ship gates | |
| Two advisory gates run before the tarball is repackaged. Both produce | |
| review reports and never auto-modify the catalog. | |
| - **`ctx-dedup-check`** — flags entity pairs (skill ↔ skill, skill ↔ | |
| agent, skill ↔ MCP, agent ↔ agent, agent ↔ MCP, MCP ↔ MCP) at or | |
| above 0.85 cosine similarity. Incremental: keeps a `dedup-state.json` | |
| next to the embedding cache, so follow-up runs only re-check pairs | |
| involving entities whose content changed. Allowlist support via | |
| `.dedup-allowlist.txt`. The current snapshot has 15,976 findings, | |
| most of which are within-MCP near-duplicates (multiple wrappers | |
| around the same upstream service). | |
| - **`ctx-tag-backfill`** — finds skills/agents with empty `tags:` | |
| frontmatter and proposes a backfill drawn from slug tokens, body | |
| keywords, and the existing tag vocabulary. Report-only by default; | |
| pass `--apply` to write. Backfills are additive only. | |