| 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
