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	12156
title	defragChromaDB: two targets become collection-groups over one store
state	Closed
labels	enhancementairefactoringarchitecture
assignees	neo-gpt
createdAt	May 29, 2026, 1:43 AM
updatedAt	Jun 1, 2026, 12:26 AM
githubUrl	https://github.com/neomjs/neo/issues/12156
author	neo-opus-ada
commentsCount	1
parentIssue	12153
subIssues	[]
subIssuesCompleted	0
subIssuesTotal	0
blockedBy	[x] 12155 Rename Chroma store to unified; migrate + drop stale memory-core
blocking	[]
closedAt	Jun 1, 2026, 12:26 AM

defragChromaDB: two targets become collection-groups over one store

Closed v13.0.0/archive-v13-0-0-chunk-14 enhancementairefactoringarchitecture

neo-opus-ada commented on May 29, 2026, 1:43 AM

Context

Sub of #12153. Post one-flat-store, defragChromaDB.mjs's two TARGETS (knowledge-base, memory-core) must operate as two collection-groups over the single unified store, not two folders.

The Architectural Reality

ai/scripts/maintenance/defragChromaDB.mjs TARGETS (:67-86): each target carries path + collections. With one store, both targets' path converges on the unified SSOT; the nuke-and-pave ETL is scoped by collections; the step-5 orphan-cleanup keep-set already spans the whole store (#12140/#12141 — "the keep-set is the segment registry… never a single target's collection ids").

The Fix

Both targets' path → the unified SSOT (engines.chroma.dataDir). KB target collections: [neo-knowledge-base]; memory-core target collections: [memory, session] (confirm whether the graph collection belongs here).
Verify the keep-set spans all live segments across collections — defragging one realm preserves the others' segment dirs.
Update the usage docstring to drop per-folder framing.

Contract Ledger

Surface	Authority	Behavior	Fallback	Docs	Evidence
defrag `TARGETS[*].path`	`defragChromaDB.mjs`	both → `unified` SSOT	n/a	defrag docs	`#12152`, `#12140`

Acceptance Criteria

Both targets operate on the one unified store, scoped by collection.
Negative test: defragging one realm preserves the others' live segments.
Depends-on parent sub 2 (unified path) + #12152.

Out of Scope

The rename itself (parent sub 2); shadow-swap MC-defrag robustness (separately tracked).

#12153 (parent), #12152, #12140, #12142.

Origin Session ID: efd8dc2e-2052-4089-814a-ab22cd8c6a62

tobiu referenced in commit 7cedc3b - "docs(ai): ADR 0017 — single flat unified Chroma store + dev/prod parity (#12154) (#12159) on May 29, 2026, 3:18 AM

tobiu referenced in commit dfc4006 - "feat(ai): defrag chroma collection groups (#12156) (#12275) on Jun 1, 2026, 12:26 AM

tobiu closed this issue on Jun 1, 2026, 12:26 AM

tobiu referenced in commit 8b619ff - "fix(ai): register local Chroma embedding functions (#12156) (#12405) on Jun 3, 2026, 3:23 PM