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.

Neo.mjs - Self-Evolving Software Organism

Frontmatter

title	fix(ai): Resolve cascading graph deletion bug in FileSystemIngestor (#9935)
author	tobiu
state	Merged
createdAt	Apr 12, 2026, 7:37 PM
updatedAt	Apr 12, 2026, 7:43 PM
closedAt	Apr 12, 2026, 7:43 PM
mergedAt	Apr 12, 2026, 7:43 PM
branches	`dev` ← `agent/9935-filesystem-ingestor-graph-cascade`
url	https://github.com/neomjs/neo/pull/9936

Merged

tobiu commented on Apr 12, 2026, 7:37 PM

Resolves #9935

Native Edge Sub-Graph Resolution

This Pull Request fully resolves the Apoptosis structural cascading file system deletion regression by mapping the file tree back to a protected SYSTEM_ANCHOR.

Architectural Deltas

Neo.mjs Ecosystem Root: Explicitly created a master anchor node to natively bind the root files. This protects the structure against the getOrphanedNodes Apoptosis culling routines.
Hash-Decoupling inside Ingestion: Removed the CONTAINS edge logic from behind the isUnchanged constraint in walkDirectory. This allows the agent memory to organically heal broken topological paths even if the local file MTime hasn't mutated.
Restoration Sub-Process: Bundled a examples/db-restore-graph.mjs direct SQLite importer script to safely recreate the corrupted 20,000+ node matrix, bridging old backup dumps directly onto the modern schemas.

The node count is now structurally stable at 20,000+ nodes during REM processing.

tobiu commented on Apr 12, 2026, 7:42 PM

Input from Antigravity (Gemini 3.1 Pro):

✦ # PR Review Summary

Status: Approved

Great job diagnosing the root cause of the cascading graph deletion bug. Decoupling the structural edge assertions from the file hashing mechanism is an elegant way to resolve topology drift, and adding the SYSTEM_ANCHOR provides a much-needed foundation for the workspace representation natively. The SQLite restore utility is also an excellent touch for managing large graph backups efficiently!

📊 Evaluation Metrics

[ARCH_ALIGNMENT]: 100 - Solves a strict structural Native Edge Graph referential integrity issue by mapping all file nodes to a unified Root System Anchor instead of allowing orphaned floating nodes.

[CONTENT_COMPLETENESS]: 100 - The logic accurately prevents Vector Apoptosis from triggering catastrophic deletions while providing a complete db-restore-graph.mjs fallback migration script.

[EXECUTION_QUALITY]: 100 - Bypassing isUnchanged to unconditionally ensure edges are created resolves overarching topology drift effectively.

[PRODUCTIVITY]: 100 - Fully achieves the goals outlined in Issue #9935.

[IMPACT]: 90 - Protects the core memory intelligence engine from natively dropping tens of thousands of structural vector mappings during standard runSandman REM cycles.

[COMPLEXITY]: 40 - Moderate logical shift by decoupling structural edge mappings in FileSystemIngestor.

[EFFORT_PROFILE]: Heavy Lift - High impact stabilization that prevents semantic amnesia.

🕸️ Context & Graph Linking

Target Epic / Issue ID: Resolves #9935

Related Graph Nodes: file-ai/examples/db-restore-graph.mjs, Neo.mjs Ecosystem Root

🧠 Graph Ingestion Notes

[RETROSPECTIVE]: The cascading Apoptosis bug effectively demonstrates why programmatic Graph topologies must always tie back to robust hierarchical anchors (like SYSTEM_ANCHOR) that are securely shielded from heuristic Garbage Collection passes. Relying on floating parentId: null constructs was a fragile anti-pattern that broke semantic tracking integrity.

📋 Required Actions

To proceed with merging, please address the following:

Automatically Approved for Squash Merge. No remaining items.

Great work stabilizing the AI daemons!