What is the Neural Link?

The Neural Link is a bi-directional bridge that connects AI agents directly to the Neo.mjs runtime. It lets agents inspect the Scene Graph, component state, event listeners, computed styles, and DOM rectangles, and mutate the running application in real time.

Why is Neo.mjs called an Application Engine instead of a framework?

Neo.mjs maintains persistent application objects in a worker-backed Scene Graph instead of compiling application state away into ephemeral DOM nodes. That architecture enables multi-window orchestration, runtime permutation, and deep AI introspection.

What is Context Engineering?

Context Engineering shapes the information and tool environment around AI agents. Neo.mjs implements it through Knowledge Base, Memory Core, GitHub Workflow, and Neural Link MCP servers for frontier harnesses, plus a File System MCP server for internal Neo.ai.Agent local loops.

What is the Neo.mjs Agent OS?

The Neo.mjs Agent OS is the repository Brain: source code and services for Memory Core, Knowledge Base, Active Hybrid GraphRAG, DreamService, Golden Path synthesis, A2A coordination, and Neural Link tooling.

Frontmatter

id	10032
title	ConceptService & Source Code Wiring
state	Closed
labels	enhancementaiarchitecture
assignees	tobiu
createdAt	Apr 15, 2026, 11:56 PM
updatedAt	Apr 17, 2026, 3:14 PM
githubUrl	https://github.com/neomjs/neo/issues/10032
author	tobiu
commentsCount	1
parentIssue	10030
subIssues	[]
subIssuesCompleted	0
subIssuesTotal	0
blockedBy	[x] 10031 JSONL Schema & Concept Seed Extraction
blocking	[x] 10037 ChromaDB Concept Embedding & Hybrid Search, [x] 10033 Concept Graph Unit Tests
closedAt	Apr 17, 2026, 3:14 PM

ConceptService & Source Code Wiring

Closed v13.0.0/archive-v13-0-0-chunk-4 enhancementaiarchitecture

tobiu commented on Apr 15, 2026, 11:56 PM

Objective

Build the ConceptService that loads the JSONL concept graph and provides query APIs. Wire concepts to source files via IMPLEMENTED_BY and EXPLAINED_BY edges.

Context

Phase 1, Step 2 of the Concept Ontology epic (#10030). Depends on the JSONL schema from #10031.

Deliverables

1. ConceptService Class

Location: ai/graph/ConceptService.mjs

Core APIs:

loadGraph(nodesPath, edgesPath) — Parse JSONL, build in-memory graph
getConceptTree(maxTier) — Hierarchical tree serialization
getConceptCoverage(conceptId) — Returns EXPLAINED_BY, IMPLEMENTED_BY, EXEMPLIFIED_BY edges
findGuideGaps(minWeight) — Concepts missing EXPLAINED_BY edges, sorted by weight
classifyConcept(classPath) — Which concept(s) does this class implement?
serializeForLLM(maxTier) — Compact tree format for agent context priming

2. Source Code Wiring

Script or service method that:

Walks src/**/*.mjs, extracts @class and @extends from JSDoc headers
Heuristic matching to existing concepts by package structure:
- src/data/* → "Data Layer" concept
- src/state/* → "State Provider" concept
- src/worker/* → "Worker Architecture" concept
Creates IMPLEMENTED_BY edges in edges.jsonl
Reports UNCATEGORIZED classes for review

3. Guide Wiring

Map learn/tree.json entries to the concept graph via EXPLAINED_BY edges.

4. SDK Registration

Export ConceptService from ai/services.mjs.

Weight Calculation

weight = tier_score + uniqueness_score + coverage_deficit

Tier score: 0.8 (tier 1), 0.5 (tier 2), 0.3 (tier 3)
Uniqueness: +0.2 if concept is unique to Neo.mjs
Coverage deficit: +0.3 if no EXPLAINED_BY edges

Acceptance Criteria

ConceptService loads JSONL and provides all query APIs
IMPLEMENTED_BY edges exist for major src/ classes
EXPLAINED_BY edges exist for all learn/guides/ entries
serializeForLLM() produces a compact tree under 100 lines
Registered in ai/services.mjs

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

tobiu added the enhancement label on Apr 15, 2026, 11:56 PM

tobiu added the ai label on Apr 15, 2026, 11:56 PM

tobiu added the architecture label on Apr 15, 2026, 11:56 PM

tobiu cross-referenced by #10033 on Apr 15, 2026, 11:57 PM

tobiu cross-referenced by #10034 on Apr 15, 2026, 11:57 PM

tobiu cross-referenced by #10035 on Apr 15, 2026, 11:57 PM

tobiu cross-referenced by #10036 on Apr 15, 2026, 11:58 PM

tobiu added parent issue #10030 on Apr 15, 2026, 11:58 PM

tobiu marked this issue as being blocked by #10031 on Apr 15, 2026, 11:58 PM

tobiu marked this issue as blocking #10033 on Apr 15, 2026, 11:58 PM

tobiu marked this issue as blocking #10034 on Apr 15, 2026, 11:58 PM

tobiu Apr 16, 2026, 12:11 AM

Input from Claude Opus 4.6 (Antigravity):

❋ Enhancement: Hybrid ChromaDB Integration

During planning, we identified that concept nodes (with their title + description) are ideal candidates for ChromaDB embedding as type: 'concept' documents. This enables:

queryDocuments({query: "how does reactivity work?", type: "concept"}) → ranked concept nodes by vector similarity

queryDocuments({query: "Neo.core.EffectManager", type: "concept"}) → automated IMPLEMENTED_BY wiring discovery

Cross-type semantic comparison: concept descriptions vs guide chunks → automated EXPLAINED_BY validation

Concept descriptions are short (1-3 sentences) — no semantic dilution risk. The three representations become complementary:

JSONL → structure (hierarchy, typed edges)

ChromaDB → similarity (semantic search, discovery)

SQLite Native Graph (Phase 3) → traversal (BFS, frontier routing)

Architectural note: ConceptService should live in the SDK (ai/services.mjs), not as a new MCP server. Uses KB_ChromaManager directly through SDK imports. This aligns with the wider strategy of moving business logic into the SDK and keeping MCP servers as thin transport layers.

tobiu cross-referenced by #10037 on Apr 16, 2026, 12:12 AM

tobiu marked this issue as blocking #10037 on Apr 16, 2026, 12:12 AM

tobiu cross-referenced by PR #10047 on Apr 17, 2026, 9:27 AM

tobiu assigned to @tobiu on Apr 17, 2026, 10:25 AM

tobiu referenced in commit 8cd0229 - "feat: implement ConceptService for deterministic ontology graph traversal (#10032) on Apr 17, 2026, 3:08 PM

tobiu cross-referenced by PR #10048 on Apr 17, 2026, 3:08 PM

tobiu referenced in commit 84cac1b - "feat: implement ConceptService for deterministic ontology graph traversal (#10032) (#10048) on Apr 17, 2026, 3:14 PM

tobiu closed this issue on Apr 17, 2026, 3:14 PM

tobiu cross-referenced by PR #10052 on Apr 17, 2026, 4:30 PM

tobiu cross-referenced by PR #10078 on Apr 19, 2026, 10:28 AM

tobiu cross-referenced by #10080 on Apr 19, 2026, 11:16 AM

tobiu cross-referenced by PR #10084 on Apr 19, 2026, 12:20 PM

tobiu cross-referenced by #10030 on Apr 19, 2026, 12:33 PM