Graph Integration & GapInferenceEngine Refactor

Objective

Ingest the standalone JSONL concept graph into the Native Edge Graph (SQLite) and refactor GapInferenceEngine to use deterministic concept traversal instead of regex token matching.

Context

Phase 3, Step 1 of the Concept Ontology epic (#10030). Depends on validated concept graph from Phase 1 (#10031, #10032, #10033) and visualization from Phase 2 (#10034).

Deliverables

1. DreamService Concept Ingestion

Add a new phase to DreamService (or a standalone ingestion script) that:

1. Reads .neo-ai-data/concepts/nodes.jsonl → creates/updates CONCEPT nodes in SQLite graph
2. Reads .neo-ai-data/concepts/edges.jsonl → creates typed edges (PARENT_CONCEPT, IMPLEMENTED_BY, EXPLAINED_BY, etc.)
3. Runs during DreamService Phase 0 (before gap inference)
4. Differential sync — only update changed concepts (hash comparison)

2. GapInferenceEngine Refactor

Replace the existing regex token matching in executeCapabilityGapInference() with graph traversal:

// OLD (fragile)
const hasGuide = guideFilePaths.some(p => nodeTokens.some(term => regex.test(p)));

// NEW (deterministic)
for (const concept of graphDb.getNodesByLabel('CONCEPT')) {
    const explanations = graphDb.getAdjacentNodes(concept.id, 'outbound', 'EXPLAINED_BY');
    if (explanations.length === 0 && concept.properties.weight >= threshold) {
        gaps.push({ type: 'GUIDE_GAP', concept: concept.name, weight: concept.properties.weight });
    }
}

3. Gap Types

• GUIDE_GAP: Concept has IMPLEMENTED_BY but no EXPLAINED_BY (high priority)
• EXAMPLE_GAP: Concept has EXPLAINED_BY but no EXEMPLIFIED_BY (medium priority)
• ORPHAN_CONCEPT: Concept has no IMPLEMENTED_BY edges (possible dead concept, review needed)

4. Weight-Based Prioritization

Gap priority = concept.weight × (1 - coverage). High-weight concepts missing guides float to the top of Golden Path synthesis.

Acceptance Criteria

• CONCEPT nodes visible in SQLite graph after DreamService run
• All concept edges correctly wired
• GapInferenceEngine uses graph traversal, not regex
• Gap report priorities align with concept weights
• Existing DreamService tests still pass

Origin Session ID: 496c0120-29aa-4b02-a804-d5a32ff6b5eb