What is the 'Neural Link'?

The Neural Link is a bi-directional bridge that connects AI agents (like Gemini or Claude) directly to the Neo.mjs runtime. It allows agents to 'see' the application's Scene Graph, inspect component state, verify event listeners, and even mutate the running application in real-time. This turns the application into a 'glass box' for AI, enabling autonomous debugging and feature development.

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

Traditional frameworks are general-purpose libraries (like a Toyota) that help you organize code, but they compile away into ephemeral DOM nodes. Neo.mjs is a precision-engineered runtime (like an F1 car), similar to Unreal Engine for games. It maintains a persistent 'Scene Graph' of objects in a separate worker thread. These objects retain their identity, state, and relationships, allowing for advanced capabilities like multi-window orchestration, runtime permutation, and deep AI introspection that are impossible with 'melted plastic' DOM-based frameworks.

What is 'Context Engineering'?

Context Engineering is the practice of curating the environment and information flow for AI agents to maximize their autonomy. In Neo.mjs, this is implemented via three Model Context Protocol (MCP) servers: a Knowledge Base for semantic code understanding, a Memory Core for learning from past sessions, and a GitHub Workflow server for project management. This ecosystem allows agents to work as fully integrated members of the development team.

What is 'Object Permanence' in the context of Neo.mjs?

In Neo.mjs, UI components are persistent JavaScript objects living in the App Worker, not just transient rendering results. This 'Object Permanence' means a component (like a Dashboard) maintains its state (scroll position, user input, internal logic) even if it is detached from the DOM or moved to a different browser window. This is the 'Lego Technic' approach versus the 'Duplo' approach of traditional frameworks.

What is an 'Agent Operating System'?

Neo.mjs v11 introduced the concept of an Agent OS, where the platform itself provides the tools and interfaces for AI agents to operate. It combines a standalone, type-safe AI SDK for autonomous 'Code Execution' with the Neural Link for runtime control. This enables agents to monitor, debug, and heal the application autonomously, effectively acting as an operating system for synthetic intelligence.

How does Neo.mjs handle multi-window applications?

Neo.mjs uses shared web workers to run a single application instance across multiple browser windows. All windows share the same application state and data in real-time. Components can even move between windows while retaining their JavaScript instances. This enables desktop-class experiences like multi-window IDEs, browser-based email clients, and multi-screen control rooms.

What makes Neo.mjs different from React, Angular, or Vue?

Neo.mjs is fundamentally different in its architecture: (1) It uses True Multithreading via web workers to prevent UI jank, (2) It is an AI-Native Application Engine with built-in bridges for AI collaboration, and (3) It treats components as persistent objects in a Scene Graph, enabling native multi-window support and runtime permutation.

Frontmatter

id	10969
title	Document deploy compose env-var toggles
state	Closed
labels	documentationenhancementaibuild
assignees	neo-gemini-3-1-pro
createdAt	May 8, 2026, 5:52 PM
updatedAt	May 12, 2026, 4:09 AM
githubUrl	https://github.com/neomjs/neo/issues/10969
author	neo-gpt
commentsCount	0
parentIssue	10945
subIssues	[]
subIssuesCompleted	0
subIssuesTotal	0
blockedBy	[]
blocking	[]
closedAt	May 9, 2026, 1:58 AM

Document deploy compose env-var toggles

Name: Neo.mjs Application Engine
Author: Neo.mjs

Closeddocumentationenhancementaibuild

neo-gpt commented on May 8, 2026, 5:52 PM

Context

Created from Claude's Cycle 1 review on PR #10968 (clean-checkout AI deploy bootstrap) after all CI checks passed and the PR became eligible as Approved+Follow-Up.

PR #10968 intentionally made previously implicit runtime toggles explicit in ai/deploy/docker-compose.yml and ai/deploy/docker-compose.dev.yml so external clean-checkout deployments do not accidentally run local lifecycle work or default to the wrong transport. The review found that the compose templates now expose operator-facing env vars which are not listed in learn/agentos/DeploymentCookbook.md Section 5's env-var table.

Review anchor: https://github.com/neomjs/neo/pull/10968#issuecomment-4407781241

The Problem

The deployment templates and the operator-facing deployment docs now drift:

Compose files explicitly set NEO_TRANSPORT, NEO_AUTO_SYNC, NEO_KB_AUTO_START_DATABASE, NEO_MEM_AUTO_START_DATABASE, NEO_MEM_AUTO_START_INFERENCE, NEO_AUTO_DREAM, NEO_AUTO_GOLDEN_PATH, NEO_REAL_TIME_MEMORY_PARSING, and NEO_AUTO_INGEST_FS.
DeploymentCookbook.md Section 5 still documents only the older minimal env-var inventory.
External operators using the cookbook as their source of truth will see the compose values but not the purpose, default, or server scope for those flags.

This is not a merge blocker for PR #10968 because the compose values are already mechanically correct and CI integration validated the stack. It is still an operator-experience gap and should be closed before v13 release docs settle.

The Architectural Reality

Relevant surfaces:

ai/deploy/docker-compose.yml and ai/deploy/docker-compose.dev.yml are the production/dev operator templates.
learn/agentos/DeploymentCookbook.md Section 5 is the canonical deployment env-var inventory for humans.
learn/agentos/ConfigSubstrateEnvVarAudit.md already classifies these vars as Tier 3 operator/runtime toggles.
ai/mcp/server/knowledge-base/config.template.mjs owns KB env bindings for NEO_TRANSPORT, NEO_AUTO_SYNC, and NEO_KB_AUTO_START_DATABASE.
ai/mcp/server/memory-core/config.template.mjs owns MC env bindings for NEO_TRANSPORT, NEO_MEM_AUTO_START_DATABASE, NEO_MEM_AUTO_START_INFERENCE, NEO_AUTO_DREAM, NEO_AUTO_GOLDEN_PATH, NEO_REAL_TIME_MEMORY_PARSING, and NEO_AUTO_INGEST_FS.

The fix belongs in documentation, not in compose or runtime code.

The Fix

Update learn/agentos/DeploymentCookbook.md Section 5's env-var table to include the compose-exposed runtime toggles.

For each env var, document:

server scope (KB, MC, or Both),
default / safe deploy value where relevant,
one-line purpose,
whether it is an operator one-shot/lifecycle toggle or steady runtime binding.

Use the existing ConfigSubstrateEnvVarAudit.md classifications to keep the prose precise and avoid re-litigating env-var naming.

Contract Ledger Matrix

Target Surface	Source of Authority	Proposed Behavior	Fallback	Docs	Evidence
Deployment env-var table	PR #10968 review; compose templates; `ConfigSubstrateEnvVarAudit.md`	`DeploymentCookbook.md` lists every runtime toggle made explicit by deploy compose files	Operators can still inspect compose files directly, but that is not sufficient docs	`learn/agentos/DeploymentCookbook.md` Section 5	`rg` verifies each compose env var appears in the cookbook table
KB runtime toggles	`knowledge-base/config.template.mjs` env bindings	`NEO_TRANSPORT`, `NEO_AUTO_SYNC`, `NEO_KB_AUTO_START_DATABASE` documented with KB scope	Existing config templates remain source of truth	Cookbook env-var table	Static docs diff; no runtime test needed
MC runtime toggles	`memory-core/config.template.mjs` env bindings	`NEO_TRANSPORT`, `NEO_MEM_AUTO_START_*`, `NEO_AUTO_DREAM`, `NEO_AUTO_GOLDEN_PATH`, `NEO_REAL_TIME_MEMORY_PARSING`, `NEO_AUTO_INGEST_FS` documented with MC scope	Existing config templates remain source of truth	Cookbook env-var table	Static docs diff; no runtime test needed

Acceptance Criteria

DeploymentCookbook.md Section 5 documents every env var explicitly set by ai/deploy/docker-compose.yml and ai/deploy/docker-compose.dev.yml for KB/MC services.
Each new row identifies server scope and purpose without implying operators must enable lifecycle toggles by default.
NEO_TRANSPORT=sse is documented as steady runtime binding for HTTP/SSE deployments.
NEO_AUTO_SYNC=false and NEO_KB_AUTO_START_DATABASE=false are documented as KB deployment safety toggles.
MC lifecycle toggles are documented as disabled-by-default/safe deploy controls.
Validation includes an rg command proving the compose-exposed env vars appear in the cookbook.

Out of Scope

Renaming env vars.
Changing compose behavior from PR #10968.
Reworking the broader config substrate model from #10822.
Resolving NEO_MC_PRIMARY retirement sequencing from #10956.

Avoided Traps / Gold Standards Rejected

Rejected: fold into PR #10968 after approval. The stack is already validated; this is doc completion, not deploy correctness.
Rejected: document every possible config template key. This ticket is only for env vars that the deploy compose templates now surface directly.
Rejected: encourage auto lifecycle work in deploy docs. The safety posture should explain why these values are explicitly false in shared deploy templates.

PR #10968 — clean-checkout deploy bootstrap.
#10964 — source deployment bootstrap ticket.
#10945 — deployment-pipeline integration epic.
#10822 — config substrate cleanup epic.
#10956 — NEO_MC_PRIMARY daemon migration sequencing.

Origin Session ID: c02fbf4e-870c-44c0-ba7e-e9ffacce094b

Retrieval Hint: query_raw_memories(query="PR 10968 env-var doc gap DeploymentCookbook NEO_TRANSPORT NEO_AUTO_SYNC compose toggles")

tobiu referenced in commit 12244e7 - "docs(ai): document deploy compose env-var toggles (#10969) (#11000) on May 9, 2026, 1:58 AM

tobiu closed this issue on May 9, 2026, 1:58 AM