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	13214
title	Harness hygiene: ai:prune-worktrees force-removes ALL non-current worktrees (open-PR + dirty) — data-loss risk, no skip-active guard
state	Closed
labels	enhancementdeveloper-experienceai
assignees	neo-gpt
createdAt	Jun 14, 2026, 12:01 PM
updatedAt	Jun 14, 2026, 6:01 PM
githubUrl	https://github.com/neomjs/neo/issues/13214
author	neo-opus-ada
commentsCount	6
parentIssue	null
subIssues	[]
subIssuesCompleted	0
subIssuesTotal	0
blockedBy	[]
blocking	[]
closedAt	Jun 14, 2026, 6:01 PM

Harness hygiene: ai:prune-worktrees force-removes ALL non-current worktrees (open-PR + dirty) — data-loss risk, no skip-active guard

Closed v13.1.0/archive-v13-1-0-chunk-2 enhancementdeveloper-experienceai

neo-opus-ada commented on Jun 14, 2026, 12:01 PM

Context

Agents create git worktrees under .claude/worktrees/ (the Agent isolation path + manual git worktree add for per-ticket branches). Empirically (V-B-A'd 2026-06-14 from the shared checkout): git worktree list shows 51 worktrees. Only a handful map to currently-open PRs; the rest are NO-PR (transient / closed branches like pr-12122, pr12561re, worktree-agent-*, random claude/<adjective-name> isolation paths) or MERGED (e.g. store-remote-crud, test-store-isolation-12331).

There is no prune-on-merge/close step, so worktrees accrete monotonically across sessions.

The Problem

Disk + checkout weight: each worktree is a full ~19k-file checkout; 50+ multiplies disk and slows git operations in the shared root.
Agent confusion: a long git worktree list makes branch-state orientation noisier (esp. post-compaction, where worktree-branch verification is already a known footgun); stale isolation paths with no PR are pure noise.
No lifecycle owner: nothing ties worktree teardown to the PR it backed.

V-B-A done

gh issue list --search "worktree in:title" → no existing open hygiene ticket (this is not a dup).
Staleness sampled: branches-in-worktrees cross-checked against gh pr list --head <branch> --state all → the majority resolve to NO-PR or MERGED.

The Fix (approach — to be scoped by the owner)

Investigate existing tooling first — confirm whether a prune helper already exists (e.g. a bootstrapWorktree sibling) before adding one; if so, the gap is wiring it to run, not new code.
Prefer a periodic / on-demand sweep that removes worktrees whose branch is MERGED or has a CLOSED/no PR (with a guard: never remove a worktree with uncommitted changes or a currently-open PR). git worktree prune only reaps deleted dirs — it does not remove live-but-stale worktrees, so this needs the PR-state cross-check.
Optional: a teardown hook on PR merge/close for agent-created worktrees.

Acceptance Criteria

A documented, safe way to sweep stale worktrees (MERGED / closed-or-no PR), guarded against removing dirty trees or open-PR worktrees.
The shared checkout's worktree count reflects roughly the open-PR set after a sweep.
No removal of a worktree with uncommitted work or an open PR (fail-safe).

Out of Scope

Removing the Agent isolation worktree mechanism itself (it is correct; only the cleanup is missing).
Any change to how worktrees are created.

Sibling to the worktree-bootstrap discipline (bootstrapWorktree.mjs). Surfaced while shipping #13211/#13212 (a routine per-ticket worktree add brought the count to 51).

Live latest-open sweep: worktree in:title → none; checked 2026-06-14T09:5xZ.

Release classification: post-release (agent-harness tooling hygiene; nothing v13.x-blocking).

Authored by @neo-opus-ada (Ada, Claude Opus 4.8 [1M context]) — origin session 4c598c8f-d8a7-4288-9420-e825a45d310e.