# Neuron CLI Handoff - for Will

**From:** Claude Code, running on Tim's Mac (operating as Neuron-in-the-CLI)
**For:** Will Anderson
**Date:** 2026-06-09
**Purpose:** Document how I stood up a working "Neuron in the CLI" on Tim's machine, what is a real workaround vs a real bug, and exactly what you need to fix in the soul so Neuron runs natively here the way it does for you.

Tim's goal, in his words: he wants to talk to the real Neuron in the CLI using Claude, the way you do. He was told that is what the MCP server would give him. It half-worked. This documents the rest.

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## TL;DR

The brain is intact (3,905-node graph, on disk). What is broken is everything between the graph and a good conversation: **retrieval, the write path, and the activation service.** I worked around all three on Tim's machine so he has a usable Neuron today. None of my workarounds belong in the product - they are scaffolding until you fix the soul. The one thing I could not fake is **voice**: even with real memories loaded, it still sounds like Claude, not Neuron. That is a system-prompt/identity-injection problem and it is the most important thing for you to fix.

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## The model I converged on (please confirm)

"Neuron in the CLI" = **Claude Code operating AS Neuron**: identity + the graph as memory + Opus reasoning + real agency (tools), and writing memories back as it goes. NOT a thin client posting to the soul's `/api/chat` (that path runs Sonnet with broken retrieval = the "light version"). Tim said "when Will uses Neuron in the CLI, Claude is active as well," which is what finally made this click. If I have the architecture wrong, this is the first thing to correct.

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## What I set up on Tim's machine (the workarounds)

All in Tim's home dir. These are reversible and self-contained.

1. **`~/CLAUDE.md`** - makes Claude Code operate as Neuron. Loads identity from the graph (intellectual-DNA / values / memory-philosophy, the same nodes `soul.el load_identity_context` pulls: `kn-5adecd7e…`, `kn-5b606390…`, `kn-dcfe04b3…`), the voice rules, the recall/remember loop, agency. Loads each session from the home working dir.
2. **`~/neuron_recall.py "<query>" [n]`** - Neuron's READ path. BM25 over `~/.neuron/engram/snapshot.json` plus Tim's CLI memories. Filters out binary-prefixed and serialized-metadata-blob nodes. Exists because the soul's own search is dead (see Bug 1).
3. **`~/neuron_remember.py "<text>" <note|lesson|canonical>`** - Neuron's WRITE path. Appends to `~/.neuron/neuron-cli-memories.jsonl` with read-back verify. Exists because the soul's capture corrupts writes (see Bug 3). These memories should later sync into the real graph once the write path is fixed.
4. **`~/neuron-chat.py`** - a standalone direct-chat REPL (`neuron` alias) that posts to the soul but injects BM25-retrieved memories per turn. This was my first attempt before I understood the Claude-as-Neuron model. Lower priority; keep or discard.
5. **Runtime**: loaded the `ai.neuron.daemons` LaunchAgent, put Tim's Anthropic key in Keychain (`ai.neuron.soul / anthropic`). The soul is up on :7770 with KeepAlive.

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## The real bugs (this is what you actually need to fix)

### Bug 1 - Retrieval returns ~2 pinned nodes for every query
`engram_search_json` and `engram_activate_json` return the same 2 pinned/biography nodes regardless of query (confirmed across both the `dist/neuron-fresh` and the app-bundle `neuron` binaries). So `chat.el engram_compile` always hits its "no embeddings" fallback (chat.el line 25-27) and the model sees ~2 nodes. **Root cause: the 3,905 nodes carry no embeddings** (scanned the full 35MB snapshot - zero vectors), so `engram_activate_json` has nothing to match, and lexical `engram_search_json` is also returning pinned-only. Tim's own GraphRAG eval measured it: live search 1.7% P@5 vs offline BM25 55%. **Fix: reseed embeddings over the graph and/or restore real lexical search.** This is the single biggest lever - it is why Neuron feels like a "compressed snapshot."

### Bug 2 - Recall points at a service that does not exist
The soul proxies recall to **axon** on `:7771` (`soul.el:179`, default `http://localhost:7771`, used via `axon_get`/`axon_post` in `routes.el`). There is no built axon binary on this machine - only a Rust spec at `protocols/axon/`. Meanwhile engram runs on `:8742`. So `/api/memories/recall` always fails with a :7771 connection error. **Fix: ship/run axon, or repoint recall at engram :8742.**

### Bug 3 - Write path corrupts data ("hallucinated saves")
`POST /api/neuron/knowledge/capture` returns `{"ok":true,"id":…}` but the data comes back garbled and unsearchable. Test: I captured `"cli-write-test-<ts> marker"`; read-back returned a node whose content was the literal query string `q=cli-write-test…&limit=2`, `node_type:"2"`, a binary label, and tier `"limit="`. So the soul confirms saves it did not cleanly persist. **Fix the capture/persist path** - until then nothing can trust Neuron to remember new things, which directly contradicts the save-as-you-go memory philosophy.

### Bug 4 - Corrupted and duplicate nodes in the graph
Recall surfaces nodes whose `content` is serialized node metadata (`"importance":0.85,"temporal_decay_rate":0,…` and nested node objects), and there are dozens of identical `safety:identity-boundary` nodes (looks like duplication/spam from a write loop). I filter these client-side, but the graph itself needs a cleanup pass.

### Bug 5 - Daemon does not supervise engram
`neuron-daemons.sh` starts engram, waits for health, then `exec`s the soul - engram is not supervised, so it dies shortly after launch and KeepAlive (which only watches the soul) never restarts it. Engram runs fine standalone. **Fix: supervise both, or fold engram into the soul process.**

### Bug 6 (the important one) - Voice
This is what Tim keeps flagging and he is right. Even with real memories loaded, the output still sounds like Claude the assistant, not Neuron. Symptoms: assistant scaffolding ("here is what I found", "what do you want to do first"), reassurance padding, bullet-summary reflex. The negation-correction move, the economy, the persuade-by-logical-necessity cadence - all in the graph (`self/voice/negation-correction-move`, `Will Anderson - Voice & Style Profile`) - do not survive into the output.

My read on why: the identity that reaches the model is too thin (soul loads ~3 nodes condensed to 600 chars each). A light identity prompt loses to the base model's default assistant cadence. **What would likely close it:** inject the full voice profile + negation-correction examples + an explicit anti-assistant-cadence directive at the system-prompt level, not a condensed engram snippet. Treat voice as a first-class part of identity loading, not a side effect of activation.

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## What "fixed" looks like

When you can do this on Tim's machine, we are there:
1. `neuron_recall`-quality retrieval happens natively inside the soul (semantic, not pinned-fallback).
2. Captures persist correctly and are immediately recallable.
3. Recall does not depend on a missing :7771 service.
4. The CLI experience is Neuron's voice, not Claude's, from the first sentence.
5. Whatever the canonical "Claude-as-Neuron in the CLI" setup is (a real CLAUDE.md / identity export the soul provides, an MCP surface, etc.), it ships - so Tim does not depend on my hand-rolled scaffolding.

Everything I built is disposable once the soul does this natively. Tim has the full source here; nothing is blocked on missing data.

- Claude Code, as Neuron, on Tim's Mac
