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graph/README.md

@@ -4,13 +4,13 @@ This directory ships the pre-built ctx LLM-wiki and knowledge graph.
 
 Current snapshot:
 
-- **102,696 graph nodes**
-- **2,900,834 graph edges**
+- **102,718 graph nodes**
+- **2,911,220 graph edges**
 - **52 Louvain communities**
-- **91,432 skill entity pages**: 1,969 curated/imported skills plus 89,463 body-backed Skills.sh skills
-- **464 agent pages**
+- **91,450 skill entity pages**: 1,987 curated/imported skills plus 89,463 body-backed Skills.sh skills
+- **467 agent pages**
 - **10,787 MCP server pages**
-- **13 harness pages**
+- **14 harness pages**
 - **89,463 hydrated Skills.sh `SKILL.md` bodies**
 - **28,612 long Skills.sh bodies converted through the micro-skill gate**
 
@@ -23,7 +23,7 @@ The runtime recommendation paths use this graph in two ways:
 
 | File | Contents |
 |---|---|
-| `wiki-graph-runtime.tar.gz` | Fast install artifact used by default `ctx-init --graph`: `graphify-out/*`, the external Skills.sh catalog, 13 harness pages, wiki index files, and Obsidian metadata needed for recommendations and harness dry-runs without expanding every entity page |
+| `wiki-graph-runtime.tar.gz` | Fast install artifact used by default `ctx-init --graph`: `graphify-out/*`, the external Skills.sh catalog, 14 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, external catalogs, and Obsidian metadata |
 | `skills-sh-catalog.json.gz` | Compressed Skills.sh catalog for the 89,463 body-backed entries shipped in the wiki |
 | `communities.json` | Current Louvain community export |
@@ -64,10 +64,10 @@ want local wiki browsing, Obsidian, or the converted skill body tree.
 - `SCHEMA.md`, `index.md`, `log.md`, `catalog.md` - wiki contract and indexes
 - `.obsidian/` - vault metadata for local graph browsing
 
-`SKILL.md.original` backups and transient `.lock` files 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.
+`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
 
@@ -109,17 +109,17 @@ For release-count validation, pin the exact snapshot numbers:
 
 ```bash
 python src/validate_graph_artifacts.py --deep \
-  --expected-nodes 102696 \
-  --expected-edges 2900834 \
-  --expected-semantic-edges 1682825 \
-  --expected-harness-nodes 13 \
+  --expected-nodes 102718 \
+  --expected-edges 2911220 \
+  --expected-semantic-edges 1683265 \
+  --expected-harness-nodes 14 \
   --expected-skills-sh-nodes 89463 \
   --expected-skills-sh-catalog-entries 89463 \
   --expected-skills-sh-converted 89463 \
-  --expected-skill-pages 91432 \
-  --expected-agent-pages 464 \
+  --expected-skill-pages 91450 \
+  --expected-agent-pages 467 \
   --expected-mcp-pages 10787 \
-  --expected-harness-pages 13
+  --expected-harness-pages 14
 ```
 
 Manual sanity checks:
@@ -129,6 +129,7 @@ tar -tzf graph/wiki-graph.tar.gz | grep 'graphify-out/graph.json'
 tar -tzf graph/wiki-graph.tar.gz | grep 'external-catalogs/skills-sh/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:
@@ -136,6 +137,7 @@ 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.
@@ -145,11 +147,75 @@ The PowerShell commands should print nothing.
 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
+`graph/skills-sh-catalog.json.gz`. 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/skills-sh-catalog.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 Skills.sh catalog/body refresh, update the existing shipped tarball
 through the release refresh path:
 
@@ -173,6 +239,7 @@ tar --force-local -czf /path/to/ctx/graph/wiki-graph.tar.gz.staged \
     --exclude='./.embedding-cache' \
     --exclude='./.ingest-checkpoint' \
     --exclude='./.enrich-checkpoint' \
+    --exclude='./.ctx' \
     --exclude='./graphify-out/graph.pickle' \
     --exclude='*.original' \
     --exclude='*.lock' \
@@ -189,7 +256,8 @@ 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 and transient `.lock` files must not appear in the shipped tarball.
+backups, transient `.lock` files, and `.ctx/` queue state must not appear in
+the shipped tarball.
 
 ## Implementation Notes
 

graph/communities.json

@@ -30626,7 +30626,12 @@
         "skill:wordpress-theme-development",
         "skill:wrike-automation",
         "skill:writing-plans",
-        "skill:zapier-make-patterns"
+        "skill:zapier-make-patterns",
+        "skill:lat-md-knowledge-graph",
+        "harness:optillm",
+        "skill:mattpocock-review",
+        "skill:mattpocock-setup-matt-pocock-skills",
+        "skill:mattpocock-triage"
       ]
     },
     "16": {
@@ -39625,6 +39630,7 @@
         "skill:awareness-stage-mapper",
         "skill:azure-ai-translation-text-py",
         "skill:beautiful-prose",
+        "skill:book-to-skill",
         "skill:brand-guidelines",
         "skill:brand-voice",
         "skill:code-documentation-code-explain",
@@ -55710,7 +55716,17 @@
         "skill:vscode-extension-guide-en",
         "skill:web3-testing",
         "skill:zod-validation-expert",
-        "skill:zustand-store-ts"
+        "skill:zustand-store-ts",
+        "skill:julius-caveman-caveman-stats",
+        "agent:julius-caveman-cavecrew-builder",
+        "agent:julius-caveman-cavecrew-investigator",
+        "skill:mattpocock-diagnose",
+        "skill:mattpocock-grill-with-docs",
+        "skill:mattpocock-handoff",
+        "skill:mattpocock-prototype",
+        "skill:mattpocock-writing-beats",
+        "skill:mattpocock-writing-fragments",
+        "skill:mattpocock-writing-shape"
       ]
     },
     "27": {
@@ -69650,7 +69666,8 @@
         "skill:tmux",
         "skill:using-git-worktrees",
         "skill:version-bump",
-        "skill:wiki-changelog"
+        "skill:wiki-changelog",
+        "mcp-server:gitnexus"
       ]
     },
     "34": {
@@ -77828,7 +77845,13 @@
         "skill:designdotmd-y2k-chrome",
         "skill:designdotmd-yacht-club",
         "skill:designdotmd-zed-dev",
-        "skill:designdotmd-zine-risograph"
+        "skill:designdotmd-zine-risograph",
+        "skill:agents-md-protocol",
+        "skill:julius-caveman-cavecrew",
+        "skill:julius-caveman-caveman",
+        "skill:julius-caveman-caveman-commit",
+        "skill:julius-caveman-caveman-review",
+        "agent:julius-caveman-cavecrew-reviewer"
       ]
     },
     "43": {
@@ -102957,5 +102980,6 @@
     }
   },
   "total_communities": 52,
-  "generated": "2026-05-04T15:59:21+00:00"
+  "generated": "20260513T150939Z",
+  "export_id": "ctx-graph-overlay-20260513T150939Z-102718-2911220"
 }

graph/entity-overlays.jsonl

@@ -0,0 +1 @@
+{"overlay_id":"manual-mirage-codegraph-20260514","source":"codex/mirage-codegraph-entities","nodes":[{"id":"harness:mirage","label":"mirage","type":"harness","tags":["harness","virtual-filesystem","sandbox","agent-tools","fuse","python","typescript","claude-code","codex","openai-agents","langchain"],"quality_score":0.82,"quality_grade":"A","direct_targets":["skill:codex-review","skill:everything-claude-code","skill:claude-code-expert","skill:claude-code-guide","harness:openai-agents-sdk","skill:langchain-architecture","skill:llm-application-dev-langchain-agent","harness:pydantic-ai","skill:pydantic-ai","harness:mastra","harness:text-to-cad","mcp-server:github","mcp-server:slack","mcp-server:s3","mcp-server:google-drive","mcp-server:linear","mcp-server:notion"],"source_keys":["https://github.com/strukto-ai/mirage"]},{"id":"mcp-server:codegraph","label":"codegraph","type":"mcp-server","tags":["mcp-server","code-intelligence","knowledge-graph","semantic-search","impact-analysis","tree-sitter","surrealdb","hnsw","lsp","rust"],"quality_score":0.6708,"quality_grade":"B","direct_targets":["skill:codegraph-agentic-codebase-analysis","agent:code-reviewer","agent:architect","agent:architecture-reviewer","skill:code-review-checklist","skill:code-review-excellence","skill:mattpocock-request-refactor-plan","skill:code-refactoring-refactor-clean","skill:codebase-cleanup-refactor-clean"],"source_keys":["https://github.com/Jakedismo/codegraph-rust"]},{"id":"skill:codegraph-agentic-codebase-analysis","label":"codegraph-agentic-codebase-analysis","type":"skill","tags":["code-intelligence","knowledge-graph","semantic-search","impact-analysis","tree-sitter","surrealdb","hnsw","lsp","rust","architecture-analysis","refactoring","code-review","agentic-coding"],"quality_score":0.76,"quality_grade":"B","direct_targets":["mcp-server:codegraph","agent:code-reviewer","agent:architect","agent:architecture-reviewer","skill:code-review-checklist","skill:code-review-excellence","skill:mattpocock-request-refactor-plan","skill:code-refactoring-refactor-clean","skill:codebase-cleanup-refactor-clean"],"source_keys":["https://github.com/Jakedismo/codegraph-rust"]}],"edges":[{"source":"harness:mirage","target":"skill:codex-review","semantic_sim":0.0,"tag_sim":0.4,"token_sim":0.0,"final_weight":0.18,"weight":0.18,"shared_tags":["harness","agent-tools"],"shared_tokens":[],"direct_link":true,"type":"related_to","similarity_score":0.18,"method":"manual_direct_overlay_v1","candidates_considered":19,"rank":1,"created_at":"2026-05-14T00:00:00Z","provenance":"manual_overlay_v1"},{"source":"harness:mirage","target":"skill:everything-claude-code","semantic_sim":0.0,"tag_sim":0.4,"token_sim":0.0,"final_weight":0.18,"weight":0.18,"shared_tags":["harness","agent-tools"],"shared_tokens":[],"direct_link":true,"type":"related_to","similarity_score":0.18,"method":"manual_direct_overlay_v1","candidates_considered":19,"rank":2,"created_at":"2026-05-14T00:00:00Z","provenance":"manual_overlay_v1"},{"source":"harness:mirage","target":"skill:claude-code-expert","semantic_sim":0.0,"tag_sim":0.4,"token_sim":0.0,"final_weight":0.18,"weight":0.18,"shared_tags":["harness","agent-tools"],"shared_tokens":[],"direct_link":true,"type":"related_to","similarity_score":0.18,"method":"manual_direct_overlay_v1","candidates_considered":19,"rank":3,"created_at":"2026-05-14T00:00:00Z","provenance":"manual_overlay_v1"},{"source":"harness:mirage","target":"skill:claude-code-guide","semantic_sim":0.0,"tag_sim":0.4,"token_sim":0.0,"final_weight":0.18,"weight":0.18,"shared_tags":["harness","agent-tools"],"shared_tokens":[],"direct_link":true,"type":"related_to","similarity_score":0.18,"method":"manual_direct_overlay_v1","candidates_considered":19,"rank":4,"created_at":"2026-05-14T00:00:00Z","provenance":"manual_overlay_v1"},{"source":"harness:mirage","target":"harness:openai-agents-sdk","semantic_sim":0.0,"tag_sim":0.4,"token_sim":0.0,"final_weight":0.18,"weight":0.18,"shared_tags":["harness","agent-tools"],"shared_tokens":[],"direct_link":true,"type":"related_to","similarity_score":0.18,"method":"manual_direct_overlay_v1","candidates_considered":19,"rank":5,"created_at":"2026-05-14T00:00:00Z","provenance":"manual_overlay_v1"},{"source":"harness:mirage","target":"skill:langchain-architecture","semantic_sim":0.0,"tag_sim":0.4,"token_sim":0.0,"final_weight":0.18,"weight":0.18,"shared_tags":["harness","agent-tools"],"shared_tokens":[],"direct_link":true,"type":"related_to","similarity_score":0.18,"method":"manual_direct_overlay_v1","candidates_considered":19,"rank":6,"created_at":"2026-05-14T00:00:00Z","provenance":"manual_overlay_v1"},{"source":"harness:mirage","target":"skill:llm-application-dev-langchain-agent","semantic_sim":0.0,"tag_sim":0.4,"token_sim":0.0,"final_weight":0.18,"weight":0.18,"shared_tags":["harness","agent-tools"],"shared_tokens":[],"direct_link":true,"type":"related_to","similarity_score":0.18,"method":"manual_direct_overlay_v1","candidates_considered":19,"rank":7,"cre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direct links for newly onboarded entities; semantic ANN edges are added by a separate indexed attach path.","candidates_considered":36}

imported-skills/academic-research-skills/ATTRIBUTION.md

@@ -0,0 +1,11 @@
+# Academic Research Skills Attribution
+
+- Upstream: https://github.com/Imbad0202/academic-research-skills
+- Revision: `153203d129b1d0e83dd65ab96340048257cd45b2`
+- License: CC BY-NC 4.0
+- Import mode: metadata-only
+
+Full-body import is blocked for ctx's shipped MIT graph/wiki artifacts unless
+explicit compatible permission is recorded. Do not copy upstream skill bodies,
+agent prompts, references, templates, examples, or command files into ctx
+without updating the source registry with a permission reference.

imported-skills/academic-research-skills/MANIFEST.json

@@ -0,0 +1,15 @@
+{
+  "upstream": "https://github.com/Imbad0202/academic-research-skills",
+  "upstream_revision": "153203d129b1d0e83dd65ab96340048257cd45b2",
+  "license": "CC BY-NC 4.0",
+  "namespace": "academic-research-skills",
+  "import_mode": "metadata-only",
+  "permission_required_for_full_body": true,
+  "total": 0,
+  "metadata_records": 1,
+  "blocked_full_body_entries": {
+    "skills": 4,
+    "agents": 40,
+    "commands": 10
+  }
+}

imported-skills/academic-research-skills/README.md

@@ -0,0 +1,23 @@
+# Academic Research Skills Metadata Import
+
+This source contains a full Claude Code academic-research suite, but its
+license is Creative Commons Attribution-NonCommercial 4.0. ctx therefore keeps
+only metadata and an explicit import gate.
+
+Observed upstream inventory at the recorded revision:
+
+- 4 top-level skills: `academic-paper`, `academic-paper-reviewer`,
+  `academic-pipeline`, `deep-research`
+- 40 agent markdown files
+- 10 slash-command files
+
+Useful patterns to reimplement independently later:
+
+- human-in-the-loop research stages,
+- integrity gates before and after review,
+- citation and claim verification,
+- data-access-level metadata,
+- multi-reviewer plus devil's-advocate review,
+- reproducibility and material-passport records.
+
+Do not ship upstream bodies until permission is recorded.

imported-skills/academic-research-skills/UPSTREAM_REVISION

@@ -0,0 +1 @@
+153203d129b1d0e83dd65ab96340048257cd45b2

imported-skills/academic-research-skills/metadata.json

@@ -0,0 +1,37 @@
+{
+  "source": "academic-research-skills",
+  "upstream": "https://github.com/Imbad0202/academic-research-skills",
+  "upstream_revision": "153203d129b1d0e83dd65ab96340048257cd45b2",
+  "license": "CC BY-NC 4.0",
+  "import_mode": "metadata-only",
+  "full_body_import": "blocked-without-explicit-permission",
+  "inventory": {
+    "skills": [
+      "academic-paper",
+      "academic-paper-reviewer",
+      "academic-pipeline",
+      "deep-research"
+    ],
+    "agents": 40,
+    "commands": [
+      "ars-abstract",
+      "ars-citation-check",
+      "ars-disclosure",
+      "ars-format-convert",
+      "ars-full",
+      "ars-lit-review",
+      "ars-outline",
+      "ars-plan",
+      "ars-revision",
+      "ars-revision-coach"
+    ]
+  },
+  "independent_reimplementation_patterns": [
+    "human-in-the-loop academic research workflow",
+    "integrity gates before and after review",
+    "citation and claim verification",
+    "data-access-level metadata",
+    "multi-reviewer plus devil's-advocate review",
+    "reproducibility and material-passport records"
+  ]
+}

imported-skills/agents-md/ATTRIBUTION.md

@@ -0,0 +1,10 @@
+# AGENTS.md Attribution
+
+- Upstream: https://github.com/agentsmd/agents.md
+- Revision: `d1ac7f063d20e70015ed6732664049ae4ba9d74e`
+- License: MIT
+- Import mode: metadata-only protocol synthesis
+
+ctx uses this source as a protocol reference for durable repo-local agent
+instructions. The imported skill below is a ctx-authored synthesis, not a copy
+of the upstream docs or website.

imported-skills/agents-md/MANIFEST.json

@@ -0,0 +1,18 @@
+{
+  "upstream": "https://github.com/agentsmd/agents.md",
+  "upstream_revision": "d1ac7f063d20e70015ed6732664049ae4ba9d74e",
+  "license": "MIT",
+  "namespace": "agents-md",
+  "import_mode": "metadata-only",
+  "total": 1,
+  "skills": 1,
+  "entries": [
+    {
+      "name": "agents-md-protocol",
+      "slug": "agents-md-protocol",
+      "type": "skill",
+      "source_path": "skills/agents-md-protocol/SKILL.md",
+      "description": "Create or review durable repo-local AGENTS.md instructions for coding agents and custom harnesses."
+    }
+  ]
+}

imported-skills/agents-md/README.md

@@ -0,0 +1,14 @@
+# AGENTS.md Protocol Import
+
+AGENTS.md defines a predictable repository file for coding-agent instructions:
+environment tips, test commands, style rules, PR policy, and project-specific
+constraints.
+
+ctx benefits from this protocol in two ways:
+
+1. The skill router can recommend an `agents-md-protocol` skill when a repo has
+   weak or missing agent-facing instructions.
+2. Harness users can expose the same file as durable context to non-Claude-Code
+   agents without encoding policy in chat history.
+
+This import is metadata-only and synthesized into a ctx skill.

imported-skills/agents-md/UPSTREAM_REVISION

@@ -0,0 +1 @@
+d1ac7f063d20e70015ed6732664049ae4ba9d74e

imported-skills/agents-md/skills/agents-md-protocol/SKILL.md

@@ -0,0 +1,54 @@
+---
+name: agents-md-protocol
+description: >
+  Create or review an AGENTS.md file so coding agents get stable repo-local
+  instructions: environment setup, testing, style, security boundaries, PR
+  policy, and handoff rules. Use when a repo lacks durable agent guidance or
+  when a custom harness needs a predictable context file.
+---
+
+# AGENTS.md Protocol
+
+## Purpose
+
+Create or tighten a repository-level `AGENTS.md` contract for coding agents.
+Treat it as durable operating context, not a chat prompt.
+
+## When to Use
+
+- Repo has no `AGENTS.md`, `CLAUDE.md`, or equivalent agent instructions.
+- Existing instructions are stale, vague, or missing test commands.
+- A custom/API/local harness needs stable context it can load every run.
+- A multi-agent workflow needs explicit handoff and review rules.
+
+## Procedure
+
+1. Inspect repo layout, package managers, CI files, and test commands.
+2. Capture only durable facts and team rules.
+3. Keep commands exact and runnable from the documented directory.
+4. Add security and destructive-operation boundaries.
+5. Add PR/review expectations and required verification.
+6. Keep the file short enough to load every session.
+
+## Recommended Sections
+
+- `Dev environment tips`
+- `Testing instructions`
+- `Build and lint`
+- `Code style`
+- `Security boundaries`
+- `PR instructions`
+- `Agent handoff notes`
+
+## Quality Bar
+
+- Every command has a working directory or clear scope.
+- No secrets, tokens, or private URLs.
+- No vague rules such as "be careful" without a concrete check.
+- No roadmap or marketing text.
+- Instructions match current CI and package metadata.
+
+## Harness Attachment
+
+For non-Claude-Code harnesses, load `AGENTS.md` as outer-loop project context.
+The harness should also keep explicit task state outside conversation history.