dna-sync

name	dna_sync
description	Protocol for synchronizing the Virgo DNA temporal ledger. Enforces the Audit → Sync → Verify pipeline using the Archaeology Engine.

DNA Sync Skill (Virgo DNA Edition)

Context

The Virgo DNA visualization is powered by a Temporal Ledger (src/visualizations/dna-history-backfill-v*.json). This ledger records every "epoch" (commit) that modifies the Knowledge Base or GEMINI.md.

This skill governs the mandatory 3-phase protocol for maintaining the graph's integrity.

Node Group Convention (Source of Truth)

Group	Role	Visual
999	Root Hub (GEMINI.md)	Large, solid dark blue
0	Ghosts (Untriaged/New KIs)	Small, grey, translucent
1	Virgo DNA (Core Protocols)	Purple
2	Personal Site (Visualization Sync)	Cyan
3	Spirit Research Lab (Infra)	Amber

[!IMPORTANT] Group assignments are maintained in src/visualizations/ki-groups.json. New KIs default to Group 0 (Ghost) until manually triaged in that file.

The 3-Phase Pipeline

Phase 1 — Audit

npm run dna:audit

• Compares the latest JSON ledger against the physical files in the Knowledge Base.
• Detects Zombies (deleted files still in ledger) and Ghosts (new files missing from ledger).
• MANDATORY: Fix all "Unregistered" errors in ki-groups.json before proceeding.

Phase 2 — Archaeology Sync

npm run dna:sync

• Incremental update. Extracts the last hash from the ledger and fetches only new commits.
• Generates a new versioned JSON file in src/visualizations/.
• MANDATORY GATE: Ensure the "Virgo Archaeology" log reports successful epoch extraction.

Phase 3 — Visual Verification

• Open the Virgo DNA Showcase page (/virgo-dna).
• Verify that the latest changes are reflected in the "Neural Trace" (the playback graph).
• Confirm that Group 1 nodes are correctly labeled as Virgo DNA.

Archaeological Protocol (Flag Economy)

dna-archaeology.ts is the engine. It supports the following flags:

• --sync: (Default) Resume from the last known commit.
• --fresh: Full reconstruction from Genesis. Use only if history logic changes.
• --partial <n>: Process only the most recent <n> commits.
• --scope <paths>: Comma-separated paths to track (Default: Knowledge Base + GEMINI.md).

Post-Sync Checklist

• Run dna:audit to confirm zero inconsistencies.
• Verify the new .json file is present in src/visualizations/.
• Check that PromptArchitectureSpace.tsx correctly generates GitHub links for new epochs.