feat(cli): Claude-as-Neuron CLI tooling + soul-side handoff

Tooling built on Tim's machine to run Neuron from the terminal as a
Claude Code session (identity + graph memory + agency) instead of
relaying to the soul's /api/chat.

- cli/neuron_recall.py    BM25 read over the engram snapshot + CLI memories
                          (works around pinned-only soul search)
- cli/neuron_remember.py  reliable local memory writes with read-back verify
                          (works around the corrupting capture endpoint)
- cli/neuron-chat.py      standalone direct-chat REPL with per-turn memory injection
- cli/neuron_mcp.py       stdlib MCP server (chat/search) with graceful degradation
- cli/CLAUDE.md.example   the operating identity that makes Claude Code run as Neuron
- cli/HANDOFF.md          soul-side bugs to fix so this becomes unnecessary

Scaffolding/proposal - intended to be retired once the soul does native
retrieval, correct persistence, and a real CLI identity/voice surface.
Pairs with the runtime model-passthrough + UTF-8 fixes in the el repo.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

cli/README.md

@@ -0,0 +1,42 @@
+# Neuron in the CLI (Claude-as-Neuron)
+
+Tooling for running Neuron from the terminal as a Claude Code session, rather than
+relaying to the soul's `/api/chat`. Built on Tim's machine 2026-06-09. Treat this as a
+proposal: it is scaffolding that works around current soul limitations, and most of it
+should be retired once the soul does these things natively.
+
+## The model
+
+"Neuron in the CLI" = Claude Code operating **as** Neuron: the soul/graph provide identity
+and memory, Claude Code provides reasoning and agency (real tools, plus writing memories
+back). Posting to the soul's non-agentic `/api/chat` gives the "light version" (Sonnet,
+plus the retrieval problems below), so this approach puts the reasoning in Claude Code and
+reads/writes the graph directly.
+
+## Files
+
+- **`CLAUDE.md.example`** - the operating identity. Placed at a session's working-dir root
+  (e.g. `~/CLAUDE.md`), it makes Claude Code load Neuron's identity from the graph
+  (intellectual-DNA / values / memory-philosophy), hold the voice rules, and run the
+  recall/remember loop. Example contains Tim-specific context; genericize before reuse.
+- **`neuron_recall.py "<query>" [n]`** - READ path. BM25 over
+  `~/.neuron/engram/snapshot.json` plus local CLI memories. Filters binary-prefixed and
+  serialized-metadata nodes. Exists because the soul's in-process search returns ~2 pinned
+  nodes for every query.
+- **`neuron_remember.py "<text>" <note|lesson|canonical>`** - WRITE path. Appends to
+  `~/.neuron/neuron-cli-memories.jsonl` with read-back verify. Exists because the soul's
+  `/api/neuron/knowledge/capture` corrupts/loses writes. These should sync into the graph
+  once the write path is fixed.
+- **`neuron-chat.py`** - standalone direct-chat REPL that posts to the soul but injects
+  BM25-retrieved memories per turn. Earlier approach, kept for reference.
+- **`neuron_mcp.py`** - stdlib MCP server exposing `neuron_chat`, `neuron_search_knowledge`,
+  `neuron_search_memory` to Claude Code, with graceful degradation when the soul's memory
+  recall backend is down.
+- **`HANDOFF.md`** - full writeup of what was set up and the soul-side bugs to fix
+  (retrieval/embeddings, the missing axon :7771 service, the write path, daemon engram
+  supervision, and voice).
+
+## What should replace this
+
+When the soul does native semantic retrieval, persists captures correctly, and exposes a
+real identity/voice surface for the CLI, these scripts become unnecessary. See `HANDOFF.md`.