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	9579
title	Fix ChromaDB defrag crash on ghost entries
state	Closed
labels	bugai
assignees	tobiu
createdAt	Mar 27, 2026, 2:30 PM
updatedAt	Mar 27, 2026, 2:35 PM
githubUrl	https://github.com/neomjs/neo/issues/9579
author	tobiu
commentsCount	2
parentIssue	null
subIssues	[]
subIssuesCompleted	0
subIssuesTotal	0
contentTrust
projected
quarantined	0
signals	[]
blockedBy	[]
blocking	[]
closedAt	Mar 27, 2026, 2:31 PM

Fix ChromaDB defrag crash on ghost entries

Closed v12.1.0/archive-v12-1-0-chunk-3 bugai

tobiu commented on Mar 27, 2026, 2:30 PM

The ai:defrag-kb and Memory Core defrag tools crash with Internal error: Error finding id on corrupted instances containing ghost entries. This completely blocks the "Nuke & Pave" defragmentation strategy. The extraction algorithm was rewritten to isolate and drop corrupted ghost entries while rescuing the valid ones, bypassing the ChromaDB batch extraction failure.

tobiu Mar 27, 2026, 2:30 PM

Input from Gemini 3.1 Pro (Antigravity):

✦ Fixed via commit. The defragChromaDB.mjs script now successfully identifies and skips ghost entries, rescuing valid items and drastically reducing file bloat (demonstrated ~89% reduction in testing).

tobiu Mar 27, 2026, 2:35 PM

Input from Gemini 3.1 Pro (Antigravity):

✦ Pushed an additional commit to refine the ghost entry log output into a single combined summary line, and added this ticket to the v12.1.0 release notes.

2026-05-28T17:58:25Z @neo-gpt cross-referenced by PR #12141