Neo.mjs Architecture Overview

Neo has four areas a reader should keep separate before the details start:

• Body: the multi-threaded application engine in neomjs/neo that runs apps off the main thread.
• Brain: the Agent OS in neomjs/neo-agent-brain: Memory Core, Knowledge Base, Native Edge Graph, Dream Pipeline, Golden Path, and the orchestration substrate around them.
• Neural Link: the possession bridge between the Brain and a live Neo application Body.
• Deployment topology: LOCAL Agent OS for one developer, or CLOUD Agent OS for a shared team service. This is separate from whether the models themselves run locally or remotely.

This guide is the ecosystem map across those areas. It shows how the Brain consumes the Body's class system, how the Brain keeps one unified Chroma topology for logical Knowledge Base and Memory Core collections, and how Neural Link lets the Brain inhabit a running Neo application without turning repository learning into a browser-runtime requirement.

For setup and configuration of individual MCP servers, see the dedicated guides linked at the bottom of this document.

The Two Hemispheres

Neo.mjs is one organism across two sibling repositories. Its hemispheres share a common nervous system — the Neo Class System:

Both hemispheres are built on the same Neo.core.Base class system. DreamService, GraphService, Agent, Loop, and every MCP service extend Neo.core.Base and use Neo.setupClass() exactly like Neo.button.Base or Neo.grid.Container. The Brain is a separate package and repository, but it remains a native consumer and inhabitant of the Engine it maintains.

Left Hemisphere: The Runtime Engine

The runtime is Neo's core value proposition. All application logic runs off the Main Thread inside a multi-worker architecture:

Key Concepts

• App Worker: Hosts all components, controllers, state providers, and business logic. This is where your application code lives.
• VDom Worker: A dedicated thread for the JSON diff engine. It receives VDOM blueprints from the App Worker and computes minimal delta updates.
• Data Worker: Handles stores, models, sorting, filtering, and grouping — keeping heavy data operations off the main thread.
• Main Threads: Thin clients that only apply DOM mutations. Each browser window has its own main thread, but they all connect to the same App Worker.

The Triangular Optimization

VDOM updates follow an optimized triangular path:

1. App Worker sends the new JSON VDOM tree to the VDom Worker
2. The Main Thread intercepts the VDom Worker's reply and applies delta mutations to the DOM immediately
3. Main Thread forwards confirmation back to the App Worker

This eliminates a full round-trip vs naively routing updates through the App Worker.

SharedWorker Mode

When useSharedWorkers: true, the App Worker becomes a SharedWorker. Multiple browser windows connect to the same App Worker instance, sharing a single JavaScript heap. Components can be moved between windows — unmounted from one, remounted in another — without losing state. This is the foundation of Neo's multi-window application support.

Right Hemisphere: The Agent OS

The Agent OS is a Node.js infrastructure that provides AI agents with persistent memory, semantic understanding of the codebase, peer coordination, and optional access to a live Neo application through Neural Link:

The Chroma process is unified. Knowledge Base and Memory Core do not run separate ChromaDBs; they use separate logical collections against the shared Chroma backend. The orchestrator owns that Chroma lifecycle in deployed topologies, while each server connects as a client through its own ChromaManager.

LOCAL Brain vs. CLOUD Brain

The Agent OS has two deployment topologies:

• LOCAL Agent OS: a single developer's on-machine Brain beside a checkout. It is private by default, simple to iterate on, and useful for solo maintenance.
• CLOUD Agent OS: a shared, tenant-scoped team Brain around one or more repositories. It gives the team shared Memory Core, shared Knowledge Base, shared A2A, and shared diagnostics.

There is no guide-level conversion path between them. They are two topologies of the same organism. A team chooses the topology that matches its collaboration boundary.

Model placement is a separate choice. A local Agent OS can call a remote Gemini provider while bootstrapping. A cloud Agent OS can use a local OpenAI-compatible or Ollama provider when privacy, cost, or residency requires it. The provider axes are role-specific: chat/summaries, embeddings, Dream graph generation, and Knowledge Base answer synthesis can each be routed deliberately.

The Cognitive Loop

The agent runtime (ai/agent/Loop.mjs) implements a four-phase cognitive loop:

1. Perceive: The ContextAssembler fetches long-term memory (session summaries via RAG), short-term memory (recent session history), and skill metadata to build the LLM context window.
2. Reason: The assembled context is sent to the configured model provider for inference, producing a response that may include tool calls.
3. Act: Tool calls are executed via the MCP protocol (for frontier models) or the SDK (for sub-agents with Zod validation).
4. Reflect: Every thought, decision, and tool call is persisted via add_memory(), creating the episodic memory record that the DreamService will later digest.

The SDK Bouncer Pattern

The SDK is two barrels, one safety layer. ai/services.host.mjs serves the host plane and ai/services.mjs serves the cloud plane while re-exporting the host services, so it remains the composition root for containerised work. Both load OpenAPI specs from each MCP server and wrap each method with makeSafe() — a function that generates Zod validators at startup.

The validating-Proxy machinery lives below both barrels, so a service is the same Proxy instance whichever barrel imports it. The split exists because a host process has only the base package tier: importing the cloud root eagerly reaches packages it does not have, and a host entrypoint must not be able to reach a durable store by import alone. See ADR 0039 — including why that property needs both a static walk and a runtime denial witness, and why neither alone establishes it.

• Frontier models access services via MCP protocol (stdio) with unbounded tool access.
• Sub-agents access the same services via the SDK, but every call is runtime-validated against the OpenAPI schema, preventing hallucinated JSON from reaching internal databases.

MCP Server Surfaces

Those MCP servers are tool surfaces, not the whole Brain. Long-running background work lives in ai/daemons/: the orchestrator schedules Dream, Golden Path, tenant repo sync, memory summary backfill, graph-log compaction, primary-dev sync, swarm heartbeat, and the data-integrity self-healing sweeps. Keep those inventories separate: an orchestrator data-integrity service is not an MCP server, and a model provider is not a daemon.

The Neural Link Bridge

The Neural Link is the connection point between the two hemispheres. It allows the Agent OS to reach into the running browser application:

The AI does not scrape DOM. It queries the semantic component tree directly — asking for components by ntype, reading store data, inspecting state providers, and even hot-patching methods on class prototypes at runtime. The same WebSocket bridge serves both AI agents and Playwright test fixtures, creating a unified "Whitebox E2E" testing architecture.

How it Works

1. The Neo.ai.Client singleton lives inside the App Worker (browser-side)
2. It connects to the Neural Link MCP Server via WebSocket (JSON-RPC 2.0)
3. The MCP Server exposes 5 client-side service categories: Component, Data, Instance, Interaction, and Runtime
4. When a new browser window connects, the client rehydrates the full window topology to the Agent OS

The Dream Pipeline

The DreamService is an autonomous background daemon that runs when agents are idle. It is the mechanism by which the system learns from itself:

The Six Phases

1. File Ingest: FileSystemIngestor.syncWorkspaceToGraph() scans the repository and ingests issues, markdown files, and source files into the Native Edge Graph (SQLite).

2. Tri-Vector Extraction: The configured graph provider analyzes undigested session memories and extracts three vectors: semantic graph nodes and edges, the feature namespace being worked on, and any roadmap impact.

3. Topological Conflict Detection: Another LLM pass scans for tickets that have been rendered obsolete, superseded, or duplicated by recent session decisions. Alerts are written to sandman_handoff.md.

4. Capability Gap Inference: This phase is deterministic — it does not use an LLM. It cross-references structural code nodes and concept-ontology nodes against explicit graph evidence:

   • Does test/ contain files with precise evidence for this class's semantic name tokens? If not: TEST_GAP; if yes, add a VALIDATES edge from the test FILE node to the structural source node.
   • Does a high-weight CONCEPT node have an outbound EXPLAINED_BY edge to a guide/doc file? If not: GUIDE_GAP. Concepts with guide coverage but no EXEMPLIFIED_BY edge become EXAMPLE_GAP.

5. Hebbian Decay: Universal edge weight fade and garbage collection of stale nodes, inspired by synaptic pruning in neuroscience.

6. Golden Path Synthesis: Tri-Vector scoring of all OPEN issues, producing a prioritized roadmap written to sandman_handoff.md. This file is the strategic dashboard that the next agent instance reads on boot.

The Closed Loop

This is the architecture's gravitational center. Every piece connects into a single self-improving feedback loop:

The Golden Path (sandman_handoff.md) is an advisory forecast, not a work queue: peer maintainers self-select what to work on, while the human operator steers direction and holds the merge gate rather than assigning tickets.

The agent's improvements to the codebase also improve the agent's knowledge base, which improves the agent's future decisions. This is what distinguishes Neo.mjs from tools that provide memory, orchestration, or multi-agent roles in isolation — Neo builds the complete organism where the codebase and the agent co-evolve.

Structural Inventory

Runtime Engine (Browser)

Agent OS (Brain repository)

All paths in this table are relative to the sibling neomjs/neo-agent-brain repository, including its canonical src/** domains. They are separate from the Engine's src/** packages listed above.

Post-M6 (#10986) the per-MCP-server services were lifted from ai/mcp/server/<name>/services/ into the flat SDK boundary at ai/services/<name>/. The ai/mcp/server/<name>/ directories now host only the server entry-point (Server.mjs), config templates, logger, and shared helpers; the service implementations live under ai/services/<name>/. Both rows are listed below for navigability.

Harness (the Agent Harness's native vessel)

Architectural Decision Records

The Agent OS subsystem records its load-bearing architectural trade-offs in learn/agentos/decisions/. Every cross-system trade-off — i.e. one that touches multiple subsystems, sets a precedent for future code, or affects load-bearing invariants — earns an ADR (per the structural-pre-flight skill's Strategy-vs-Tactics threshold). Per-class localized constraints stay inline as Anchor & Echo guards instead.

The map-as-pointer principle: the Structural Inventory above links each subsystem row to its relevant ADRs so readers who follow the map naturally encounter the architectural-decision substrate without needing to remember to consult decisions/ separately. Authors of new ADRs MUST add the link to the affected Structural Inventory rows in the same PR (per #10449 Sub-Issue 2 / structural-pre-flight map-maintenance discipline).

This table is a curated subset — map-relevant highlights, deliberately NOT the complete corpus index. The authoritative every-ADR composition map is ADR 0031's seam table, kept complete by construction via the lint-adr-seam-table CI guard (one row per present ADR, enforced both directions). A new ADR always takes its seam-table row (CI fails otherwise) and additionally earns a row here only when it affects mapped Structural Inventory rows.

Next Steps

• Deploying the Agent OS — Benefit-altitude path into the cloud-deployment guide set
• Why Deploy the Agent OS — The cloud-deployment hub and ordered learning path
• Strategic Workflows — Advanced agent workflow patterns
• Swarm Intelligence & Sub-Agents — Delegation, profiles, and capability gating
• The Dream Pipeline & Golden Path — Forecasting engine and scoring algorithm
• Neural Link: Live Application Mutability — Deep dive into the Neural Link bridge
• The Knowledge Base Server — Semantic RAG architecture
• The Memory Core Server — Episodic memory and graph storage
• Self-Healing Immune System — Detect, diagnose, and bounded autonomous recovery
• The GitHub Workflow Server — Offline-first issue management
• Code Execution (AI SDK) — The SDK Bouncer pattern in detail