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	9912
title	bug(ai): Prevent Vector Apoptosis from eradicating structural entities
state	Closed
labels	bugaicore
assignees	tobiu
createdAt	Apr 12, 2026, 1:37 PM
updatedAt	Apr 12, 2026, 9:25 PM
githubUrl	https://github.com/neomjs/neo/issues/9912
author	tobiu
commentsCount	0
parentIssue	null
subIssues	[]
subIssuesCompleted	0
subIssuesTotal	0
blockedBy	[]
blocking	[x] 9914 Epic: Native Edge Graph Auditing and Deduplication Pipeline
closedAt	Apr 12, 2026, 9:20 PM

bug(ai): Prevent Vector Apoptosis from eradicating structural entities

Closed v13.0.0/archive-v13-0-0-chunk-3 bugaicore

tobiu commented on Apr 12, 2026, 1:37 PM

Context

runSandman.mjs is unnecessarily re-embedding every OPEN issue and discussion during the REM extraction pipeline. We originally suspected sqlite-vec metadata formatting, but the root cause is that GraphService.getOrphanedNodes() considers any node without edges to be "orphaned" and permanently deletes it via Vector Apoptosis.

Objective

Update GraphService.getOrphanedNodes() to explicitly protect structural entities like ISSUE, DISCUSSION, and PULL_REQUEST from apoptosis, so they remain in the Native Edge Graph and ChromaDB, successfully passing the hash equality bypass on subsequent runs.

tobiu added the bug label on Apr 12, 2026, 1:37 PM

tobiu added the ai label on Apr 12, 2026, 1:37 PM

tobiu added the core label on Apr 12, 2026, 1:37 PM

tobiu marked this issue as blocking #9914 on Apr 12, 2026, 1:40 PM

tobiu referenced in commit 24fcafc - "fix(ai): Protect structural graph nodes from Vector Apoptosis (#9912)" on Apr 12, 2026, 9:19 PM

tobiu cross-referenced by PR #9941 on Apr 12, 2026, 9:20 PM

tobiu referenced in commit 39c378a - "fix(ai): Protect structural graph nodes from Vector Apoptosis (#9912) (#9941)" on Apr 12, 2026, 9:20 PM

tobiu closed this issue on Apr 12, 2026, 9:20 PM

tobiu changed title from bug(ai): Debug sqlite-vec metadata schema to restore DreamService Hash Bypass to bug(ai): Prevent Vector Apoptosis from eradicating structural entities on Apr 12, 2026, 9:24 PM

tobiu assigned to @tobiu on Apr 12, 2026, 9:25 PM