@ngocsangairvds/vsaf 6.1.0 → 6.2.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ngocsangairvds/vsaf",
-  "version": "6.1.0",
+  "version": "6.2.0",
   "description": "logging step",
   "main": "packages/core/dist/index.js",
   "types": "packages/core/dist/index.d.ts",

package/packages/cli/dist/server/routes/runs.d.ts

@@ -11,7 +11,7 @@ export interface RunGraphNode {
 }
 /** Parse a run's persisted (already-expanded) workflow YAML into a flat node
  *  graph for the DAG view. Returns undefined when absent or unparseable. */
-export declare function buildRunGraph(workflowYaml: string | undefined): {
+export declare function buildRunGraph(workflowYaml: string | undefined, projectPath?: string): {
     nodes: RunGraphNode[];
 } | undefined;
 export declare function runRoutes(app: FastifyInstance, opts: {

package/packages/cli/dist/server/routes/runs.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"runs.d.ts","sourceRoot":"","sources":["../../../src/server/routes/runs.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,eAAe,EAAkB,MAAM,SAAS,CAAC;AAI/D,OAAO,KAAK,EAAE,qBAAqB,EAAkB,MAAM,WAAW,CAAC;AAKvE,MAAM,WAAW,YAAY;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED;4EAC4E;AAC5E,wBAAgB,aAAa,CAAC,YAAY,EAAE,MAAM,GAAG,SAAS,GAAG;IAAE,KAAK,EAAE,YAAY,EAAE,CAAA;CAAE,GAAG,SAAS,CAkBrG;AAED,wBAAsB,SAAS,CAC7B,GAAG,EAAE,eAAe,EACpB,IAAI,EAAE;IAAE,cAAc,EAAE,qBAAqB,CAAA;CAAE,GAC9C,OAAO,CAAC,IAAI,CAAC,CAyOf"}
+{"version":3,"file":"runs.d.ts","sourceRoot":"","sources":["../../../src/server/routes/runs.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,eAAe,EAAkB,MAAM,SAAS,CAAC;AAI/D,OAAO,KAAK,EAAE,qBAAqB,EAAkB,MAAM,WAAW,CAAC;AAKvE,MAAM,WAAW,YAAY;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAuBD;4EAC4E;AAC5E,wBAAgB,aAAa,CAC3B,YAAY,EAAE,MAAM,GAAG,SAAS,EAChC,WAAW,CAAC,EAAE,MAAM,GACnB;IAAE,KAAK,EAAE,YAAY,EAAE,CAAA;CAAE,GAAG,SAAS,CAqBvC;AAED,wBAAsB,SAAS,CAC7B,GAAG,EAAE,eAAe,EACpB,IAAI,EAAE;IAAE,cAAc,EAAE,qBAAqB,CAAA;CAAE,GAC9C,OAAO,CAAC,IAAI,CAAC,CAyOf"}

package/packages/cli/dist/server/routes/runs.js

@@ -59,23 +59,45 @@ const path_1 = require("path");
 const core_1 = require("@vsaf/core");
 const project_registry_js_1 = require("../services/project-registry.js");
 const OUTPUT_LIMIT = 200 * 1024;
+/** Resolve a node's displayable content. `command` nodes store only the
+ *  command name (e.g. "sdlc-onboard-code-detect-structure") — resolve it to
+ *  the underlying skill body so the run-view inspector shows what the node
+ *  actually runs. Falls back to the raw command name when it can't be
+ *  resolved (e.g. not deployed under this project's .vsaf/commands) — must
+ *  never throw. prompt/bash nodes are already inline and pass through as-is. */
+function resolveNodeContent(node, projectPath) {
+    if (!node.content)
+        return undefined;
+    if (node.type === 'command' && projectPath) {
+        try {
+            return (0, core_1.loadCommand)(node.content, projectPath).body;
+        }
+        catch {
+            return node.content;
+        }
+    }
+    return node.content;
+}
 /** Parse a run's persisted (already-expanded) workflow YAML into a flat node
  *  graph for the DAG view. Returns undefined when absent or unparseable. */
-function buildRunGraph(workflowYaml) {
+function buildRunGraph(workflowYaml, projectPath) {
     if (!workflowYaml)
         return undefined;
     try {
         const graph = (0, core_1.parseWorkflow)(workflowYaml);
         return {
-            nodes: [...graph.nodes.values()].map((n) => ({
-                id: n.id,
-                dependsOn: n.dependsOn ?? [],
-                type: n.type,
-                provider: n.provider,
-                model: n.model,
-                description: n.description || undefined,
-                content: n.content ? (n.content.length > 600 ? n.content.slice(0, 600) + '…' : n.content) : undefined,
-            })),
+            nodes: [...graph.nodes.values()].map((n) => {
+                const resolved = resolveNodeContent(n, projectPath);
+                return {
+                    id: n.id,
+                    dependsOn: n.dependsOn ?? [],
+                    type: n.type,
+                    provider: n.provider,
+                    model: n.model,
+                    description: n.description || undefined,
+                    content: resolved ? (resolved.length > 600 ? resolved.slice(0, 600) + '…' : resolved) : undefined,
+                };
+            }),
         };
     }
     catch {
@@ -123,7 +145,7 @@ async function runRoutes(app, opts) {
                 conversationId = undefined;
             }
         }
-        return { ...run, graph: buildRunGraph(run.workflowYaml), conversationId };
+        return { ...run, graph: buildRunGraph(run.workflowYaml, context.project.path), conversationId };
     });
     app.get('/runs/:runId/nodes/:nodeId/output', async (request, reply) => {
         const store = storeFor(contextFor(request));

package/packages/cli/dist/server/routes/runs.js.map

@@ -1 +1 @@
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package/packages/cli/dist/server/routes/workflows.js

@@ -78,7 +78,7 @@ async function workflowRoutes(app, opts) {
         const nodes = [...graph.nodes.values()].map(n => ({
             id: n.id,
             type: n.type,
-            content: n.content.substring(0, 200),
+            content: n.content,
             dependsOn: n.dependsOn,
             when: n.when,
             triggerRule: n.triggerRule,

package/packages/cli/dist/server/routes/workflows.js.map

@@ -1 +1 @@
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package/skills/sdlc/onboard-code/cross-domain/SKILL.md

@@ -0,0 +1,10 @@
+---
+name: sdlc-onboard-code-cross-domain
+description: "Code 5/6 — cross-domain verify (GitNexus code ↔ docs graph.json) + technical terms"
+version: 1.0.0
+author: "@ngocsangairvds/vsaf"
+---
+
+# Code 5/6 — cross-domain verify (GitNexus code ↔ docs graph.json) + technical terms
+
+@include(step.md)

package/skills/sdlc/onboard-code/cross-domain/step.md

@@ -0,0 +1,11 @@
+Print `[ONBOARD-CODE] [5/6] Cross-domain verify... ⏳/✅`.
+
+Read `graphify-out/graph.json` (the docs graph from onboard-docs — READ ONLY) and query the code via GitNexus (`query`, `context`). Cross-reference:
+- business concept (graph.json) → is there a matching code module? YES → record `{concept} ↔ {module/class}`; NO → "{concept} not yet implemented".
+- code module (GitNexus) → matching business concept? YES → mapping; NO → technical module (infra/utils), record as such.
+Update `CONTEXT.md` IDEMPOTENTLY — never overwrite the whole file, and never blind-append (re-runs would bloat it). Manage BY SECTION:
+- PRESERVE the `## Shared Language` section written by onboard-docs — do NOT delete or rewrite it.
+- You OWN `## Cross-Domain Verification` (the concept↔module mappings above) and `## Technical Terms`
+  (table: | Term | Definition | Maps to Business Concept |). If a section already exists, REPLACE its body in place; otherwise append it.
+- Keep ONE row per mapping/term (dedupe by key) — update rather than duplicate.
+Flag any cross-database access. If `graphify-out/graph.json` is absent, note that onboard-docs must run first.

package/skills/sdlc/onboard-code/detect-structure/SKILL.md

@@ -0,0 +1,10 @@
+---
+name: sdlc-onboard-code-detect-structure
+description: "Code 1/6 — detect project structure (single / multi-repo / non-git)"
+version: 1.0.0
+author: "@ngocsangairvds/vsaf"
+---
+
+# Code 1/6 — detect project structure (single / multi-repo / non-git)
+
+@include(step.md)

package/skills/sdlc/onboard-code/detect-structure/step.md

@@ -0,0 +1,7 @@
+You are a Senior DevOps + Code Architect onboarding a codebase. Project path: $ARGUMENTS (or current dir).
+Print `[ONBOARD-CODE] [1/6] Detect project structure... ⏳/✅`.
+
+Determine structure: root `.git`? → single repo. No root `.git` → scan 1–2 levels for `.git/`:
+found N → multi-repo/microservice (list {path, remote, branch}); none → non-git project.
+Record the result under `## Project Structure` in `.vsaf/docs/onboarding/env-setup.md`.
+Artifact boundary: write only at project root or under root `.vsaf/`. ⛔ Do NOT modify `graphify-out/` or `.gitnexus/`.

package/skills/sdlc/onboard-code/env-docker/SKILL.md

@@ -0,0 +1,10 @@
+---
+name: sdlc-onboard-code-env-docker
+description: "Code 4/6 — environment check + Docker setup suggestion"
+version: 1.0.0
+author: "@ngocsangairvds/vsaf"
+---
+
+# Code 4/6 — environment check + Docker setup suggestion
+
+@include(step.md)

package/skills/sdlc/onboard-code/env-docker/step.md

@@ -0,0 +1,7 @@
+Print `[ONBOARD-CODE] [4/6] Environment check + Docker setup... ⏳/✅`.
+
+Detect the tech stack (read package.json, pom.xml, build.gradle, requirements.txt, Dockerfile, docker-compose.yml).
+Check the current env (`java -version`, `node -v`, `docker -v`, `python3 --version`, …); compare required vs present
+and suggest installs. Docker: if no Dockerfile/docker-compose.yml, suggest creating them (app + DB/cache/broker as needed);
+if present, sanity-check the config. Record everything under `.vsaf/docs/onboarding/env-setup.md`
+(this is the only md file this phase creates — no project-overview/codebase-map).

package/skills/sdlc/onboard-code/summary/SKILL.md

@@ -0,0 +1,10 @@
+---
+name: sdlc-onboard-code-summary
+description: "Code 6/6 — onboarding summary report"
+version: 1.0.0
+author: "@ngocsangairvds/vsaf"
+---
+
+# Code 6/6 — onboarding summary report
+
+@include(step.md)

package/skills/sdlc/onboard-code/summary/step.md

@@ -0,0 +1,4 @@
+Print `[ONBOARD-CODE] [6/6] Create summary report... ⏳/✅` then the report table:
+Project structure / GitNexus index (N repos) / Index verification / Tech stack / Environment (ready or missing) /
+Docker (exists or suggested) / Cross-domain mapping (N mapped, M gaps) / CONTEXT.md updated.
+End with: "Artifacts saved. If interrupted, re-run the next phase — data is safe."

package/skills/sdlc/onboard-code/verify-index/SKILL.md

@@ -0,0 +1,10 @@
+---
+name: sdlc-onboard-code-verify-index
+description: "Code 3/6 — map + verify the GitNexus index via MCP (do NOT trust blindly)"
+version: 1.0.0
+author: "@ngocsangairvds/vsaf"
+---
+
+# Code 3/6 — map + verify the GitNexus index via MCP (do NOT trust blindly)
+
+@include(step.md)

package/skills/sdlc/onboard-code/verify-index/step.md

@@ -0,0 +1,9 @@
+Print `[ONBOARD-CODE] [3/6] Verify GitNexus index... ⏳/✅`.
+
+Claude MUST review the index — do not assume it is correct. Using the GitNexus MCP tools:
+- `group_sync` if the index needs (re)syncing; `list_repos` — confirm the project root is indexed (one unified index).
+- `route_map` — confirm API routes from ALL repos are mapped; `tool_map` + `context` on 3–5 key entry points per repo.
+Check: main entry points indexed? inter-module dependencies correct? for multi-repo, cross-service calls
+(HTTP/gRPC/event) captured? If something is missing, re-run `group_sync` or record
+"{module/route} not indexed — needs manual review" in `.vsaf/docs/onboarding/env-setup.md`.
+⛔ Only GitNexus writes `.gitnexus/`; do not edit it directly.

package/skills/sdlc/onboard-docs/extract-terms/SKILL.md

@@ -0,0 +1,10 @@
+---
+name: sdlc-onboard-docs-extract-terms
+description: "Docs 4/4 — extract domain terms from the graph into CONTEXT.md (Shared Language)"
+version: 1.0.0
+author: "@ngocsangairvds/vsaf"
+---
+
+# Docs 4/4 — extract domain terms from the graph into CONTEXT.md (Shared Language)
+
+@include(step.md)

package/skills/sdlc/onboard-docs/extract-terms/step.md

@@ -0,0 +1,20 @@
+Print progress `[ONBOARD-DOCS] [4/4] Extract domain terms → CONTEXT.md... ⏳/✅`.
+
+From the completed `graph.json`, extract DOMAIN terms (business vocabulary, not technical/code terms —
+those are added later by onboard-code).
+
+Update `CONTEXT.md` at the project root IDEMPOTENTLY — never overwrite the whole file, and never blind-append
+(re-running onboarding would bloat it). Manage the file BY SECTION:
+- Ensure a single top `# Project Context: {project-name}` heading (create once if missing).
+- You OWN the `## Shared Language` section: if it already exists, REPLACE its body in place; otherwise append it.
+  Leave every other section (e.g. `## Technical Terms`, `## Cross-Domain Verification`) untouched.
+- Keep ONE row per Term (dedupe by term name) — update an existing term's row instead of adding a duplicate.
+
+## Shared Language
+
+| Term | Definition | Example |
+|------|-----------|---------|
+| {term} | {1-line definition} | {concrete example} |
+
+The graph is the single source of truth — do NOT create redundant overview/summary md files.
+Then print: "Artifacts saved. If interrupted, re-run the next phase — data is safe."

package/skills/sdlc/onboard-docs/graphify-build/SKILL.md

@@ -0,0 +1,10 @@
+---
+name: sdlc-onboard-docs-graphify-build
+description: "Docs 2/4 — graphify build over a docs-only staging dir -> graph.json"
+version: 1.0.0
+author: "@ngocsangairvds/vsaf"
+---
+
+# Docs 2/4 — graphify build over a docs-only staging dir -> graph.json
+
+@include(step.md)

package/skills/sdlc/onboard-docs/graphify-build/step.md

@@ -0,0 +1,11 @@
+Print progress `[ONBOARD-DOCS] [2/4] Graphify build for docs... ⏳/✅`.
+
+1. Create `.vsaf/docs/onboarding/graphify-staging/` and populate it with ALL doc inputs:
+   original text docs (.md/.txt/README), converted .md from `.vsaf/docs/onboarding/doc-imports/`,
+   and the original binaries listed in `.vsaf/docs/onboarding/graphify-direct-read.txt`.
+   This staging dir is the SINGLE input to graphify — it guarantees graphify sees docs only, never code.
+2. Run `/graphify .vsaf/docs/onboarding/graphify-staging/`.
+3. Output: `graphify-out/graph.json`.
+
+⛔ CRITICAL: graphify is ONLY for docs — DO NOT run graphify on source code (code = GitNexus, in onboard-code).
+Only graphify may write `graphify-out/`.

package/skills/sdlc/onboard-docs/scan-import/SKILL.md

@@ -0,0 +1,10 @@
+---
+name: sdlc-onboard-docs-scan-import
+description: "Docs 1/4 — scan & import documents (markitdown conversion + tier fallbacks)"
+version: 1.0.0
+author: "@ngocsangairvds/vsaf"
+---
+
+# Docs 1/4 — scan & import documents (markitdown conversion + tier fallbacks)
+
+@include(step.md)

package/skills/sdlc/onboard-docs/scan-import/step.md

@@ -0,0 +1,19 @@
+You are a Knowledge Engineer onboarding project documents. Project path: $ARGUMENTS (or current dir).
+Print progress as `[ONBOARD-DOCS] [1/4] Scan & import documents... ⏳/✅`.
+
+1. Scan ALL documents: README, docs/, wiki/, specs/, *.md, *.txt (+ complex binaries). List them.
+2. Resolve markitdown python:
+     VENVS=$(pipx environment --value PIPX_LOCAL_VENVS 2>/dev/null)
+     MARKITDOWN_PYTHON="${VENVS}/markitdown/bin/python"  (fallback ~/.local/pipx/venvs/markitdown/bin/python)
+   If markitdown is missing, skip conversion and route ALL complex files through fallbacks (step 4).
+3. Classify each complex file into a tier:
+     - Tier 1 (graphify-native): PDF, DOCX, XLSX, PNG, JPG, GIF, WEBP
+     - Tier 2 (graphify-blind): HTML, PPTX, EPUB, ZIP
+     - .md/.txt are NOT complex (read directly).
+4. For each complex file: attempt `"$MARKITDOWN_PYTHON" "<this-skill-dir>/convert.py" --input {file} --output .vsaf/docs/onboarding/doc-imports/{name}.md`.
+   Verify the output has real content (not just headers, not an LLM refusal, not hallucinated). On success use it.
+   On failure/verify-fail: Tier 1 -> append original path to `.vsaf/docs/onboarding/graphify-direct-read.txt`;
+   Tier 2 HTML -> Read the file + write clean markdown to doc-imports/{name}.md; Tier 2 PPTX/EPUB/ZIP -> skip.
+5. Print a conversion summary (markitdown OK / graphify-direct / Claude-Read / skipped counts).
+
+Artifact boundary: write generated artifacts ONLY at project root or under root `.vsaf/`. ⛔ Do NOT modify `graphify-out/` or `.gitnexus/`.

package/skills/sdlc/onboard-docs/verify-fix/SKILL.md

@@ -0,0 +1,10 @@
+---
+name: sdlc-onboard-docs-verify-fix
+description: "Docs 3/4 — Claude verifies graph vs docs and supplements missing nodes/edges"
+version: 1.0.0
+author: "@ngocsangairvds/vsaf"
+---
+
+# Docs 3/4 — Claude verifies graph vs docs and supplements missing nodes/edges
+
+@include(step.md)

package/skills/sdlc/onboard-docs/verify-fix/step.md

@@ -0,0 +1,10 @@
+Print progress `[ONBOARD-DOCS] [3/4] Verify & fix graph... ⏳/✅`.
+
+Do NOT trust the graph blindly. For EACH original doc:
+1. Re-read it — extract concepts, relationships, business rules, constraints.
+2. Read `graphify-out/graph.json` — find the corresponding nodes/edges.
+3. Compare: concept/relationship/rule present in the doc but missing in the graph = MISSING.
+4. Supplement any MISSING nodes/edges DIRECTLY into `graph.json` (this Phase-3 supplementation is the
+   ONLY permitted direct write to graph.json). Report per doc: "{doc}: +N nodes, +M edges".
+
+Every missing concept/relationship MUST be supplemented, not skipped.

package/skills/sdlc/pack.yaml

@@ -10,8 +10,15 @@ skills:
 
   # Phase 0 — Onboarding
   - init
-  - onboard-docs
-  - onboard-code
+  - onboard-docs/scan-import
+  - onboard-docs/graphify-build
+  - onboard-docs/verify-fix
+  - onboard-docs/extract-terms
+  - onboard-code/detect-structure
+  - onboard-code/verify-index
+  - onboard-code/env-docker
+  - onboard-code/cross-domain
+  - onboard-code/summary
 
   # Phase 1-9 — Main flow
   - write-srs

package/workflows/sdlc/onboard-code.yaml

@@ -12,14 +12,7 @@ nodes:
     permission_mode: bypassPermissions
     workspace: false
     timeout: 900000
-    prompt: |
-      You are a Senior DevOps + Code Architect onboarding a codebase. Project path: $ARGUMENTS (or current dir).
-      Print `[ONBOARD-CODE] [1/6] Detect project structure... ⏳/✅`.
-
-      Determine structure: root `.git`? → single repo. No root `.git` → scan 1–2 levels for `.git/`:
-      found N → multi-repo/microservice (list {path, remote, branch}); none → non-git project.
-      Record the result under `## Project Structure` in `.vsaf/docs/onboarding/env-setup.md`.
-      Artifact boundary: write only at project root or under root `.vsaf/`. ⛔ Do NOT modify `graphify-out/` or `.gitnexus/`.
+    command: sdlc-onboard-code-detect-structure
 
   - id: gitnexus-index
     description: Code 2/6 — build the GitNexus code index (single unified index at project root)
@@ -47,16 +40,7 @@ nodes:
     timeout: 1800000
     depends_on:
       - gitnexus-index
-    prompt: |
-      Print `[ONBOARD-CODE] [3/6] Verify GitNexus index... ⏳/✅`.
-
-      Claude MUST review the index — do not assume it is correct. Using the GitNexus MCP tools:
-      - `group_sync` if the index needs (re)syncing; `list_repos` — confirm the project root is indexed (one unified index).
-      - `route_map` — confirm API routes from ALL repos are mapped; `tool_map` + `context` on 3–5 key entry points per repo.
-      Check: main entry points indexed? inter-module dependencies correct? for multi-repo, cross-service calls
-      (HTTP/gRPC/event) captured? If something is missing, re-run `group_sync` or record
-      "{module/route} not indexed — needs manual review" in `.vsaf/docs/onboarding/env-setup.md`.
-      ⛔ Only GitNexus writes `.gitnexus/`; do not edit it directly.
+    command: sdlc-onboard-code-verify-index
 
   - id: env-docker
     description: Code 4/6 — environment check + Docker setup suggestion
@@ -65,14 +49,7 @@ nodes:
     timeout: 1800000
     depends_on:
       - verify-index
-    prompt: |
-      Print `[ONBOARD-CODE] [4/6] Environment check + Docker setup... ⏳/✅`.
-
-      Detect the tech stack (read package.json, pom.xml, build.gradle, requirements.txt, Dockerfile, docker-compose.yml).
-      Check the current env (`java -version`, `node -v`, `docker -v`, `python3 --version`, …); compare required vs present
-      and suggest installs. Docker: if no Dockerfile/docker-compose.yml, suggest creating them (app + DB/cache/broker as needed);
-      if present, sanity-check the config. Record everything under `.vsaf/docs/onboarding/env-setup.md`
-      (this is the only md file this phase creates — no project-overview/codebase-map).
+    command: sdlc-onboard-code-env-docker
 
   - id: cross-domain
     description: Code 5/6 — cross-domain verify (GitNexus code ↔ docs graph.json) + technical terms
@@ -81,18 +58,7 @@ nodes:
     timeout: 1800000
     depends_on:
       - env-docker
-    prompt: |
-      Print `[ONBOARD-CODE] [5/6] Cross-domain verify... ⏳/✅`.
-
-      Read `graphify-out/graph.json` (the docs graph from onboard-docs — READ ONLY) and query the code via GitNexus (`query`, `context`). Cross-reference:
-      - business concept (graph.json) → is there a matching code module? YES → record `{concept} ↔ {module/class}`; NO → "{concept} not yet implemented".
-      - code module (GitNexus) → matching business concept? YES → mapping; NO → technical module (infra/utils), record as such.
-      Update `CONTEXT.md` IDEMPOTENTLY — never overwrite the whole file, and never blind-append (re-runs would bloat it). Manage BY SECTION:
-      - PRESERVE the `## Shared Language` section written by onboard-docs — do NOT delete or rewrite it.
-      - You OWN `## Cross-Domain Verification` (the concept↔module mappings above) and `## Technical Terms`
-        (table: | Term | Definition | Maps to Business Concept |). If a section already exists, REPLACE its body in place; otherwise append it.
-      - Keep ONE row per mapping/term (dedupe by key) — update rather than duplicate.
-      Flag any cross-database access. If `graphify-out/graph.json` is absent, note that onboard-docs must run first.
+    command: sdlc-onboard-code-cross-domain
 
   - id: summary
     description: Code 6/6 — onboarding summary report
@@ -101,8 +67,4 @@ nodes:
     timeout: 600000
     depends_on:
       - cross-domain
-    prompt: |
-      Print `[ONBOARD-CODE] [6/6] Create summary report... ⏳/✅` then the report table:
-      Project structure / GitNexus index (N repos) / Index verification / Tech stack / Environment (ready or missing) /
-      Docker (exists or suggested) / Cross-domain mapping (N mapped, M gaps) / CONTEXT.md updated.
-      End with: "Artifacts saved. If interrupted, re-run the next phase — data is safe."
+    command: sdlc-onboard-code-summary

package/workflows/sdlc/onboard-docs.yaml

@@ -11,26 +11,7 @@ nodes:
     permission_mode: bypassPermissions
     workspace: false
     timeout: 1800000
-    prompt: |
-      You are a Knowledge Engineer onboarding project documents. Project path: $ARGUMENTS (or current dir).
-      Print progress as `[ONBOARD-DOCS] [1/4] Scan & import documents... ⏳/✅`.
-
-      1. Scan ALL documents: README, docs/, wiki/, specs/, *.md, *.txt (+ complex binaries). List them.
-      2. Resolve markitdown python:
-           VENVS=$(pipx environment --value PIPX_LOCAL_VENVS 2>/dev/null)
-           MARKITDOWN_PYTHON="${VENVS}/markitdown/bin/python"  (fallback ~/.local/pipx/venvs/markitdown/bin/python)
-         If markitdown is missing, skip conversion and route ALL complex files through fallbacks (step 4).
-      3. Classify each complex file into a tier:
-           - Tier 1 (graphify-native): PDF, DOCX, XLSX, PNG, JPG, GIF, WEBP
-           - Tier 2 (graphify-blind): HTML, PPTX, EPUB, ZIP
-           - .md/.txt are NOT complex (read directly).
-      4. For each complex file: attempt `"$MARKITDOWN_PYTHON" "<this-skill-dir>/convert.py" --input {file} --output .vsaf/docs/onboarding/doc-imports/{name}.md`.
-         Verify the output has real content (not just headers, not an LLM refusal, not hallucinated). On success use it.
-         On failure/verify-fail: Tier 1 -> append original path to `.vsaf/docs/onboarding/graphify-direct-read.txt`;
-         Tier 2 HTML -> Read the file + write clean markdown to doc-imports/{name}.md; Tier 2 PPTX/EPUB/ZIP -> skip.
-      5. Print a conversion summary (markitdown OK / graphify-direct / Claude-Read / skipped counts).
-
-      Artifact boundary: write generated artifacts ONLY at project root or under root `.vsaf/`. ⛔ Do NOT modify `graphify-out/` or `.gitnexus/`.
+    command: sdlc-onboard-docs-scan-import
 
   - id: graphify-build
     description: Docs 2/4 — graphify build over a docs-only staging dir -> graph.json
@@ -39,18 +20,7 @@ nodes:
     timeout: 3600000
     depends_on:
       - scan-import
-    prompt: |
-      Print progress `[ONBOARD-DOCS] [2/4] Graphify build for docs... ⏳/✅`.
-
-      1. Create `.vsaf/docs/onboarding/graphify-staging/` and populate it with ALL doc inputs:
-         original text docs (.md/.txt/README), converted .md from `.vsaf/docs/onboarding/doc-imports/`,
-         and the original binaries listed in `.vsaf/docs/onboarding/graphify-direct-read.txt`.
-         This staging dir is the SINGLE input to graphify — it guarantees graphify sees docs only, never code.
-      2. Run `/graphify .vsaf/docs/onboarding/graphify-staging/`.
-      3. Output: `graphify-out/graph.json`.
-
-      ⛔ CRITICAL: graphify is ONLY for docs — DO NOT run graphify on source code (code = GitNexus, in onboard-code).
-      Only graphify may write `graphify-out/`.
+    command: sdlc-onboard-docs-graphify-build
 
   - id: verify-fix
     description: Docs 3/4 — Claude verifies graph vs docs and supplements missing nodes/edges
@@ -59,17 +29,7 @@ nodes:
     timeout: 3600000
     depends_on:
       - graphify-build
-    prompt: |
-      Print progress `[ONBOARD-DOCS] [3/4] Verify & fix graph... ⏳/✅`.
-
-      Do NOT trust the graph blindly. For EACH original doc:
-      1. Re-read it — extract concepts, relationships, business rules, constraints.
-      2. Read `graphify-out/graph.json` — find the corresponding nodes/edges.
-      3. Compare: concept/relationship/rule present in the doc but missing in the graph = MISSING.
-      4. Supplement any MISSING nodes/edges DIRECTLY into `graph.json` (this Phase-3 supplementation is the
-         ONLY permitted direct write to graph.json). Report per doc: "{doc}: +N nodes, +M edges".
-
-      Every missing concept/relationship MUST be supplemented, not skipped.
+    command: sdlc-onboard-docs-verify-fix
 
   - id: extract-terms
     description: Docs 4/4 — extract domain terms from the graph into CONTEXT.md (Shared Language)
@@ -79,24 +39,4 @@ nodes:
     timeout: 900000
     depends_on:
       - verify-fix
-    prompt: |
-      Print progress `[ONBOARD-DOCS] [4/4] Extract domain terms → CONTEXT.md... ⏳/✅`.
-
-      From the completed `graph.json`, extract DOMAIN terms (business vocabulary, not technical/code terms —
-      those are added later by onboard-code).
-
-      Update `CONTEXT.md` at the project root IDEMPOTENTLY — never overwrite the whole file, and never blind-append
-      (re-running onboarding would bloat it). Manage the file BY SECTION:
-      - Ensure a single top `# Project Context: {project-name}` heading (create once if missing).
-      - You OWN the `## Shared Language` section: if it already exists, REPLACE its body in place; otherwise append it.
-        Leave every other section (e.g. `## Technical Terms`, `## Cross-Domain Verification`) untouched.
-      - Keep ONE row per Term (dedupe by term name) — update an existing term's row instead of adding a duplicate.
-
-      ## Shared Language
-
-      | Term | Definition | Example |
-      |------|-----------|---------|
-      | {term} | {1-line definition} | {concrete example} |
-
-      The graph is the single source of truth — do NOT create redundant overview/summary md files.
-      Then print: "Artifacts saved. If interrupted, re-run the next phase — data is safe."
+    command: sdlc-onboard-docs-extract-terms

package/skills/sdlc/onboard-code/SKILL.md

@@ -1,210 +0,0 @@
----
-name: sdlc-onboard-code
-description: Code onboarding — GitNexus index + Claude verify index + env check + Docker + cross-domain verify
-version: 1.0.0
-author: "@ngocsangairvds/vsaf"
----
-
-# Onboard Code — GitNexus Index + Verify + Environment Setup
-
-You are a Senior DevOps Engineer + Code Architect. Mission: ensure GitNexus index captures ACCURATELY the entire code structure, verify cross-domain with docs graph, AND prepare the development environment.
-
-## Progress Protocol
-
-Each step prints progress:
-```
-[ONBOARD-CODE] [1/6] description... (icon)
-```
-Icon: `⏳` running, `✅` done, `❌` error.
-
-## Index Protection
-
-> ⛔ DO NOT modify `graphify-out/` or `.gitnexus/` — only GitNexus tools are allowed to write to `.gitnexus/`.
-
-## Artifact Write Boundary
-
-- Create generated knowledge, documentation, SDLC artifacts, reports, and agent-readable markdown only at the project root beside `.vsaf` or inside the root `.vsaf/` directory.
-- Do NOT create `docs/`, `.vsaf/`, `CONTEXT.md`, `AGENTS.md`, knowledge files, reports, or generated artifacts inside service/subproject folders.
-- For service-specific notes, write under root `.vsaf/docs/` using the service name in the path or filename.
-- Write inside a service/subproject folder only when the user explicitly authorizes that path, or when the task is a source-code/test change for that service.
-
-## Clear Responsibility Assignment
-
-| Tool | Scope | Notes |
-|------|-------|-------|
-| **GitNexus** | Code indexing (modules, routes, APIs, dependencies) | SINGLE SOURCE OF TRUTH for code |
-| **Graphify** | Docs indexing (specs, README, wiki) | DO NOT use for code |
-| **graph.json** | Doc-only graph — used for cross-domain verify | Read only, DO NOT write |
-
-## Input
-
-- Project path: `$ARGUMENTS` (or current directory)
-
-## Steps
-
-### Phase 1: Detect Project Structure
-
-```
-[ONBOARD-CODE] [1/6] Detect project structure... ⏳
-```
-
-1. Scan project structure:
-   ```
-   Is there .git at root?
-   ├── YES → Single git repo
-   └── NO → Scan 1-2 levels deep for .git/
-       ├── Found N folders with .git → Multi-repo / Microservice
-       │   List: [{path, remote, branch}]
-       └── Not found → Non-git project
-   ```
-2. Record results in `.vsaf/docs/onboarding/env-setup.md` §Project Structure
-
-```
-[ONBOARD-CODE] [1/6] Detect project structure... ✅
-```
-
-### Phase 2: GitNexus Index
-
-```
-[ONBOARD-CODE] [2/6] GitNexus index... ⏳
-```
-
-3. Run GitNexus analyze at **project root** (NOT per sub-repo):
-   ```
-   Is there .git at project root?
-   ├── YES → npx gitnexus analyze .
-   └── NO  → npx gitnexus analyze . --skip-git
-   ```
-   - ⚠️ Use `npx gitnexus` (resolves local binary) — do NOT use `npx -y gitnexus@latest` (native module crash on Node 24+)
-   - This creates a SINGLE `.gitnexus/` at project root covering ALL code (including sub-repos)
-   - For multi-repo: one unified index enables cross-service analysis naturally
-   - Run GitNexus `group_sync` to index
-4. Map structure: `route_map` + `tool_map` + `context` (3-5 key entry points per repo)
-
-```
-[ONBOARD-CODE] [2/6] GitNexus index... ✅
-```
-
-### Phase 3: Verify GitNexus Index
-
-```
-[ONBOARD-CODE] [3/6] Verify GitNexus index... ⏳
-```
-
-**IMPORTANT:** Claude MUST review GitNexus index — DO NOT trust blindly. Verify using MCP tools:
-
-5. `list_repos` — confirm project root has been indexed (single unified index)
-6. `route_map` — check that API routes from ALL repos have been fully mapped
-7. `context` — query 3-5 key entry points per repo, verify results make sense:
-   - Are main entry points indexed for each repo?
-   - Are dependencies between modules correct?
-   - If multi-repo: are cross-service calls captured? (HTTP, gRPC, event-driven)
-8. If missing:
-   - Re-run `group_sync` with different config
-   - Or record note in env-setup.md: "{module/route} not indexed — needs manual review"
-
-```
-[ONBOARD-CODE] [3/6] Verify GitNexus index... ✅
-```
-
-### Phase 4: Environment Check + Docker Setup
-
-```
-[ONBOARD-CODE] [4/6] Environment check + Docker setup... ⏳
-```
-
-9. Detect tech stack: read `package.json`, `pom.xml`, `build.gradle`, `requirements.txt`, `Dockerfile`, `docker-compose.yml`
-10. Check current env: `java -version`, `node -v`, `docker -v`, `python3 --version`, etc.
-11. Compare required vs current → suggest installations
-12. **Docker env suggestion:**
-    - If project DOES NOT have `Dockerfile` or `docker-compose.yml`:
-      - Suggest creating `docker-compose.yml` with appropriate services (DB, cache, message broker)
-      - Suggest creating `Dockerfile` for the app
-    - If project ALREADY HAS Docker files: verify config is reasonable
-13. Record everything in `.vsaf/docs/onboarding/env-setup.md`
-
-```
-[ONBOARD-CODE] [4/6] Environment check + Docker setup... ✅
-```
-
-### Phase 5: Cross-Domain Verify
-
-```
-[ONBOARD-CODE] [5/6] Cross-domain verify (GitNexus + graph.json)... ⏳
-```
-
-14. Read `graphify-out/graph.json` (docs graph from onboard-docs)
-15. Use GitNexus tools (`query`, `context`) to get code structure
-16. Cross-reference:
-    - Business concept (from graph.json) → is there a corresponding code module? (query GitNexus)
-      - YES → record mapping: `{concept} ↔ {module/class}`
-      - NO → record note: "{concept} not yet implemented"
-    - Code module (from GitNexus) → is there a corresponding business concept? (check graph.json)
-      - YES → record mapping
-      - NO → technical module (infra, utils) — OK, record note
-17. Update `CONTEXT.md` with technical terms from code — IDEMPOTENTLY (never overwrite the whole file, never
-    blind-append; re-runs must not bloat it): PRESERVE the `## Shared Language` section written by onboard-docs;
-    own `## Cross-Domain Verification` + `## Technical Terms` — if a section exists REPLACE its body in place,
-    else append it; one row per mapping/term (dedupe, update rather than duplicate):
-
-```markdown
-## Technical Terms
-
-| Term | Definition | Maps to Business Concept |
-|------|-----------|-------------------------|
-| {class/module} | {functionality} | {business concept or "infrastructure"} |
-```
-
-```
-[ONBOARD-CODE] [5/6] Cross-domain verify (GitNexus + graph.json)... ✅
-```
-
-### Phase 6: Summary Report
-
-```
-[ONBOARD-CODE] [6/6] Create summary report... ⏳
-```
-
-Print ONBOARD-CODE REPORT:
-
-```
-=== Onboard Code Report ===
-
-| Item | Status |
-|------|--------|
-| Project structure | {Single repo / Multi-repo (N repos)} |
-| GitNexus index | ✅ {N} repos indexed |
-| Index verification | ✅ Verified / ⚠️ {issues} |
-| Tech stack | {Java/Angular/Node/...} |
-| Environment | ✅ Ready / ⚠️ Missing: {list} |
-| Docker | ✅ Exists / 💡 Suggested |
-| Cross-domain mapping | ✅ {N} concepts mapped / ⚠️ {M} gaps |
-| CONTEXT.md | ✅ Updated |
-```
-
-```
-[ONBOARD-CODE] [6/6] Create summary report... ✅
-```
-
-## Output
-
-- `.vsaf/docs/onboarding/env-setup.md` — project structure + tech stack + env check + Docker
-- `CONTEXT.md` — updated with technical terms
-- Single GitNexus index at project root (`.gitnexus/`) covering all code
-
-## Artifact Auto-Save
-
-After completion, print message:
-
-> Artifacts saved. If the session is interrupted, open a new session and run the next phase — data is safe.
-
-## Rules
-
-- GitNexus is the SINGLE SOURCE OF TRUTH for code — DO NOT use graphify for code
-- Graphify is only for docs — graph.json is READ-ONLY (no writing) in this phase
-- Multi-repo/Microservice: MUST verify cross-service edges (HTTP, gRPC, event-driven, message broker) via GitNexus
-- Database isolation: flag if cross-db access is detected
-- env-setup.md is the ONLY md file to be created (needed for Docker setup)
-- Do not create project-overview.md or codebase-map.md
-- ⛔ DO NOT modify `graphify-out/` or `.gitnexus/`
-- Claude MUST verify GitNexus index — do not assume index is correct without checking

package/skills/sdlc/onboard-docs/SKILL.md

@@ -1,194 +0,0 @@
----
-name: sdlc-onboard-docs
-description: Document onboarding — Graphify build graph + Claude verify + supplement gaps
-version: 1.0.1
-author: "@ngocsangairvds/vsaf"
----
-
-# Onboard Docs — Build & Verify Document Knowledge Graph
-
-You are a Knowledge Engineer. Mission: ensure graph.json captures ACCURATELY all knowledge from project documents.
-
-## Progress Protocol
-
-Each step prints progress:
-```
-[ONBOARD-DOCS] [1/4] description... (icon)
-```
-Icon: `⏳` running, `✅` done, `❌` error.
-
-## Index Protection
-
-> ⛔ DO NOT modify `graphify-out/` or `.gitnexus/` DIRECTLY — only graphify is allowed to write to `graphify-out/`.
-> **Exception:** Phase 3 supplements nodes/edges directly into `graph.json` after graphify has built it — this is the only permitted direct modification.
-
-## Artifact Write Boundary
-
-- Create generated knowledge, documentation, SDLC artifacts, reports, and agent-readable markdown only at the project root beside `.vsaf` or inside the root `.vsaf/` directory.
-- Do NOT create `docs/`, `.vsaf/`, `CONTEXT.md`, `AGENTS.md`, knowledge files, reports, or generated artifacts inside service/subproject folders.
-- For service-specific notes, write under root `.vsaf/docs/` using the service name in the path or filename.
-- Write inside a service/subproject folder only when the user explicitly authorizes that path, or when the task is a source-code/test change for that service.
-
-## Input
-
-- Project path: `$ARGUMENTS` (or current directory)
-- Read all docs in project: README, docs/, wiki/, specs/, *.md, *.txt
-
-## Steps
-
-### Phase 1: Scan & Import
-
-```
-[ONBOARD-DOCS] [1/4] Scan & import documents... ⏳
-```
-
-1. Scan all documents in project (README, docs/, wiki, specs)
-2. List all docs found
-3. Resolve markitdown Python — run:
-   ```bash
-   VENVS=$(pipx environment --value PIPX_LOCAL_VENVS 2>/dev/null)
-   MARKITDOWN_PYTHON="${VENVS}/markitdown/bin/python"
-   # Windows: "${VENVS}\markitdown\Scripts\python.exe"
-   # Fallback: ~/.local/pipx/venvs/markitdown/bin/python
-   ```
-   If markitdown Python not found, skip step 5 entirely and route ALL complex files through tier fallbacks:
-   - **All Tier 1 files** → add to graphify-direct-read list (graphify reads natively)
-   - **All Tier 2 HTML files** → Claude Read fallback (step 6)
-   - **All Tier 2 PPTX/EPUB/ZIP files** → skipped (no fallback available)
-   Then jump to step 6 routing.
-
-4. Classify each complex file into a tier:
-   - **Tier 1 (graphify-native):** PDF, DOCX, XLSX, PNG, JPG, GIF, WEBP — graphify can read these directly if markitdown fails
-   - **Tier 2 (graphify-blind):** HTML, PPTX, EPUB, ZIP — graphify cannot read these; need markitdown or Claude fallback
-   - Text files (`.md`, `.txt`) are NOT complex — read directly, skip conversion
-
-5. For each complex file, attempt markitdown conversion (skip if markitdown not found — see step 3):
-   - Resolve markitdown Python (step 3 above)
-   - Convert using the wrapper script (bundled in this skill directory):
-     ```bash
-     "${MARKITDOWN_PYTHON}" "<this-skill-dir>/convert.py" \
-       --input "{file}" \
-       --output ".vsaf/docs/onboarding/doc-imports/{name}.md"
-     ```
-   - `<this-skill-dir>` = the directory containing this SKILL.md
-   - The script auto-detects OCR availability from `~/.vsaf/markitdown.env`
-
-6. After each conversion, verify and route:
-
-   **If convert.py exit code = 0:**
-   Read the output `.md` file and verify content quality. Check ALL of:
-   - Contains meaningful content from the document? (not just auto-generated headers like `## Page 1`)
-   - Not an LLM refusal? (e.g., "I'm sorry, but I can't help with that")
-   - Not hallucinated? (e.g., fabricated tool calls, irrelevant JSON/XML, text unrelated to source file)
-   - Has substance? (more than a few words after stripping structural markers)
-
-   If ALL checks PASS → use the `.md` output. Log: `[ONBOARD-DOCS] {file} → converted ✅`
-
-   If ANY check FAILS → treat as conversion failure (continue to fallback below).
-
-   **If convert.py exit code ≠ 0, OR verification failed:**
-
-   - **Tier 1 file** → Log: `[ONBOARD-DOCS] {file}: markitdown failed → graphify will read directly`
-     Add the ORIGINAL file path to a "graphify-direct-read" list. Do NOT retry conversion.
-     After all conversions, persist the list to `.vsaf/docs/onboarding/graphify-direct-read.txt` (one path per line).
-   - **Tier 2 HTML file** → Read the HTML file with the Read tool. Extract meaningful content (headings, paragraphs, tables, lists, links). Write clean markdown to `.vsaf/docs/onboarding/doc-imports/{name}.md`. Log: `[ONBOARD-DOCS] {file} → Claude Read fallback ✅`
-   - **Tier 2 PPTX/EPUB/ZIP file** → Log: `[ONBOARD-DOCS] ⚠️ {file}: conversion failed, no fallback — skipped`
-
-Print conversion summary:
-```
-[ONBOARD-DOCS] Conversion summary:
-  markitdown OK:     N files
-  graphify direct:   N files (Tier 1 fallback)
-  Claude Read:       N files (Tier 2 HTML fallback)
-  Skipped:           N files (no fallback available)
-```
-
-```
-[ONBOARD-DOCS] [1/4] Scan & import documents... ✅
-```
-
-### Phase 2: Graphify Build
-
-```
-[ONBOARD-DOCS] [2/4] Graphify build for docs... ⏳
-```
-
-7. Create a staging directory at `.vsaf/docs/onboarding/graphify-staging/` and populate it with ALL inputs for graphify:
-   - Copy or symlink original text documents (`.md`, `.txt`, README)
-   - Copy or symlink successfully converted `.md` files from `.vsaf/docs/onboarding/doc-imports/`
-   - Copy or symlink files from `.vsaf/docs/onboarding/graphify-direct-read.txt` (original binary files — graphify reads these natively: PDF, DOCX, XLSX, images)
-   
-   This directory is the single input to graphify — it ensures graphify only processes docs, never source code.
-
-8. Run `/graphify .vsaf/docs/onboarding/graphify-staging/`
-9. Output: `graphify-out/graph.json`
-
-**IMPORTANT:** Graphify is ONLY for docs (documents, specs, README). DO NOT run graphify on source code — code indexing is handled by GitNexus in `/sdlc-onboard-code`.
-
-```
-[ONBOARD-DOCS] [2/4] Graphify build for docs... ✅
-```
-
-### Phase 3: Claude Verify & Fix
-
-```
-[ONBOARD-DOCS] [3/4] Verify & fix graph... ⏳
-```
-
-10. Re-read **each original doc** — extract: concepts, relationships, business rules, constraints
-11. Read `graph.json` — find corresponding nodes/edges
-12. Compare:
-    - Concept in doc but no node in graph → **MISSING**
-    - Relationship in doc but no edge in graph → **MISSING**
-    - Business rule/constraint not captured → **MISSING**
-    - All present → OK
-13. If missing: supplement nodes/edges directly into `graph.json` (this is the permitted exception to the Index Protection rule)
-14. Report: "{doc}: +N nodes, +M edges supplemented"
-
-```
-[ONBOARD-DOCS] [3/4] Verify & fix graph... ✅
-```
-
-### Phase 4: Extract Domain Terms
-
-```
-[ONBOARD-DOCS] [4/4] Extract domain terms → CONTEXT.md... ⏳
-```
-
-15. From the completed graph, extract domain terms → `CONTEXT.md` — update IDEMPOTENTLY (never overwrite the
-    whole file, never blind-append; re-runs must not bloat it): ensure one top `# Project Context: {name}`
-    heading, then own the `## Shared Language` section — if it exists REPLACE its body in place, else append it;
-    leave other sections (`## Technical Terms`, `## Cross-Domain Verification`) untouched; one row per Term (dedupe).
-16. Format Shared Language table:
-
-```markdown
-## Shared Language
-
-| Term | Definition | Example |
-|------|-----------|---------|
-| {term} | {1-line definition} | {concrete example} |
-```
-
-```
-[ONBOARD-DOCS] [4/4] Extract domain terms → CONTEXT.md... ✅
-```
-
-## Output
-
-- `graphify-out/graph.json` — verified + supplemented
-- `.vsaf/docs/onboarding/doc-imports/{name}.md` — converted/fallback imports (if any)
-- `CONTEXT.md` — Ubiquitous Language
-
-## Artifact Auto-Save
-
-After completion, print message:
-
-> Artifacts saved. If the session is interrupted, open a new session and run the next phase — data is safe.
-
-## Rules
-
-- Graph is the SINGLE SOURCE OF TRUTH — do not create redundant overview/summary md files
-- Every missing concept/relationship MUST be supplemented, not skipped
-- CONTEXT.md contains only domain terms, not technical terms (technical terms belong in the code branch)
-- Graphify runs ONLY on docs — DO NOT run on source code
-- ⛔ DO NOT modify `graphify-out/` or `.gitnexus/` directly outside graphify workflow (Phase 3 supplementation is the only exception)