neuralmind

CLI Reference

Complete command-line interface documentation for NeuralMind.

Overview
Global Options
Commands
- build
- query
- wakeup
- search
- benchmark
- stats
- validate
- doctor
- eval
- learn (deprecated)
- next
- memory
- skeleton
- last
- install-hooks
- init-hook
- watch
- serve
- daemon
Exit Codes
Environment Variables
Examples

Overview

NeuralMind provides a command-line interface for building neural indexes, querying codebases with natural language, and managing knowledge graphs.

neuralmind [OPTIONS] COMMAND [ARGS]

Getting Help

# General help
neuralmind --help

# Command-specific help
neuralmind build --help
neuralmind query --help

Global Options

Option	Description
`--help`	Show help message and exit
`--version`	Show version number

Commands

build

Build or rebuild the neural index from a knowledge graph.

neuralmind build <project_path> [OPTIONS]

Arguments

Argument	Required	Description
`project_path`	Yes	Path to project root containing `graphify-out/graph.json`

Options

Option	Default	Description
`--force`, `-f`	False	Force re-embedding of all nodes, even if unchanged

Output

Displays build statistics including:

Number of nodes processed
Number of nodes embedded (new/changed)
Number of nodes skipped (unchanged)
Number of communities indexed
Build time elapsed

Examples

# Basic build
neuralmind build /path/to/project

# Force complete rebuild
neuralmind build /path/to/project --force

Prerequisites

As of v0.15.0, none beyond pip install neuralmind. When no graphify-out/graph.json exists, build auto-generates one with the bundled tree-sitter backend (neuralmind/graphgen.py) and prints:

[neuralmind] generated code graph via the built-in tree-sitter backend → graphify-out/graph.json

Backend precedence:

A real graphify graph always takes priority where present (graphify update /path/to/project).
Otherwise the built-in tree-sitter backend generates the graph. As of v0.16.0 it indexes Python, TypeScript, and Go (.py, .ts/.tsx, .go) out of the box; more grammars register behind the SUPPORTED_SUFFIXES seam. A mixed-language repo is indexed in one pass.
--force only regenerates graphs we wrote — it never clobbers a graphify build.
An empty/non-code project writes no graph, so you still get the “no graph” guidance rather than a silent 0-node success.
Optional precision (v0.17.0+): set NEURALMIND_PRECISION=1 and place a *.scip index (from scip-python/scip-typescript/scip-go) in the project root to replace the built-in backend’s heuristic calls/inherits edges with compiler-accurate ones for the files the index covers. Off by default.

query

Query the codebase with natural language and get optimized context.

neuralmind query <project_path> "<question>" [OPTIONS]

Arguments

Argument	Required	Description
`project_path`	Yes	Path to project root
`question`	Yes	Natural language question about the codebase

Options

Option	Default	Description
`--json`, `-j`	False	Output results as JSON
`--trace`	False	(v0.23.0+) Attach a per-layer retrieval trace (see below)
`--trace-verbose`	False	(v0.23.0+) With `--trace`, keep full candidate/hit lists

Output

Returns:

Optimized context text for AI consumption
Token count and breakdown by layer
Reduction ratio compared to full codebase
Communities/modules loaded

Retrieval traces (v0.23.0+)

--trace explains why a result came back (PRD 3) — useful when retrieval surprises you. It records, layer by layer:

candidates — the raw vector-search pool (ids + scores);
cluster_scores — per-cluster score with vector-vs-synapse attribution (how much of each cluster’s score came from learned co-activation);
synapse_boost — individual co-activation boosts;
hits — the final ranked hits, flagging which were synapse-recalled;
budget — tokens per layer + reduction ratio.

Plain --trace prints a compact per-layer summary; --json includes the full trace object (bounded, and path-redactable via the RetrievalTrace API for sharing in bug reports). Tracing is off by default and zero-overhead. The daemon’s /query honors trace too, so daemon and direct mode return the same attribution.

Examples

# Basic query
neuralmind query /path/to/project "How does authentication work?"

# JSON output
neuralmind query /path/to/project "What are the main API endpoints?" --json

# Explain the retrieval path
neuralmind query /path/to/project "How does billing work?" --trace
neuralmind query /path/to/project "How does billing work?" --trace --json

Sample Output

=== Query: How does authentication work? ===

[Context]
# Project: MyApp
MyApp is a web application with JWT-based authentication...

[Authentication Module]
The auth module handles user login, token generation, and validation...

[Relevant Code]
- auth/jwt_handler.py: JWT token generation and validation
- auth/middleware.py: Authentication middleware for routes
- models/user.py: User model with password hashing

---
Tokens: 847 | Reduction: 59.0x | Layers: L0, L1, L2, L3 | Communities: [5, 12]

wakeup

Get minimal wake-up context for starting a new conversation.

neuralmind wakeup <project_path> [OPTIONS]

Arguments

Argument	Required	Description
`project_path`	Yes	Path to project root

Options

Option	Default	Description
`--json`, `-j`	False	Output results as JSON

Output

Returns L0 (Identity) + L1 (Summary) context, typically ~600 tokens, suitable for:

Starting new AI conversations
Providing project context to coding assistants
Initial system prompts

Examples

# Get wake-up context
neuralmind wakeup /path/to/project

# Redirect to file
neuralmind wakeup /path/to/project > context.md

# JSON format
neuralmind wakeup /path/to/project --json

Sample Output

=== Wake-up Context ===

# Project: MyApp

MyApp is a full-stack web application for task management built with React and Node.js.

## Architecture Overview

### Core Components
- **Frontend**: React 18 with TypeScript, Tailwind CSS
- **Backend**: Node.js/Express REST API
- **Database**: PostgreSQL with Prisma ORM
- **Auth**: JWT-based authentication

### Main Modules
1. User Management (users/) - Registration, profiles, settings
2. Task Engine (tasks/) - CRUD operations, scheduling, notifications
3. API Layer (api/) - REST endpoints, middleware, validation

---
Tokens: 412 | Layers: L0, L1

search

Perform direct semantic search across codebase entities.

neuralmind search <project_path> "<query>" [OPTIONS]

Arguments

Argument	Required	Description
`project_path`	Yes	Path to project root
`query`	Yes	Semantic search query

Options

Option	Default	Description
`--n`	10	Maximum number of results
`--json`, `-j`	False	Output results as JSON

Output

Returns matching code entities with:

Entity name and type
Similarity score (0-1)
File path
Community membership

Examples

# Basic search
neuralmind search /path/to/project "authentication"

# Limit results
neuralmind search /path/to/project "database connection" --n 5

# JSON output
neuralmind search /path/to/project "API endpoint" --json

Sample Output

=== Search: authentication ===

1. authenticate_user (function) - Score: 0.92
   File: auth/handlers.py
   Validates user credentials and returns JWT token
   Community: 5 (Authentication)

2. AuthMiddleware (class) - Score: 0.87
   File: auth/middleware.py
   Express middleware for JWT validation
   Community: 5 (Authentication)

3. hash_password (function) - Score: 0.81
   File: utils/crypto.py
   Securely hashes passwords using bcrypt
   Community: 5 (Authentication)

---
Results: 3 | Query time: 45ms

benchmark

Run performance benchmark with sample queries.

neuralmind benchmark <project_path> [OPTIONS]

Arguments

Argument	Required	Description
`project_path`	Yes	Path to project root

Options

Option	Default	Description
`--json`, `-j`	False	Output results as JSON
`--quality`	False	(v0.23.0+) Quality-eval mode — see below
`--suite`	(all)	(v0.23.0+) With `--quality`, run one suite: `python` / `typescript` / `go`
`--baseline`	—	(v0.23.0+) With `--quality`, a saved suite JSON to compare against (reports metric deltas)

Output

Comprehensive benchmark report including:

Token counts for each query type
Reduction ratios
Query latencies
Comparison with full codebase size

Examples

# Run default benchmark
neuralmind benchmark /path/to/project

# JSON output
neuralmind benchmark /path/to/project --json

Quality-eval mode (v0.23.0+)

--quality switches the command from token-reduction benchmarking to retrieval-quality measurement: does NeuralMind surface the right code, not just less of it? It scores precision@k, recall@k, MRR, and answerability over golden query suites (Python / TypeScript / Go — 30 queries with expected-module labels) and exits non-zero if a suite regresses past its floor, so CI can gate retrieval-affecting changes.

Like neuralmind eval, this is a contributor/CI self-test that runs against the golden suites shipping with the source repo (the evals/quality/ package), not the installed wheel. The pure metrics live in neuralmind.quality (from neuralmind import quality).

# Score all golden suites
neuralmind benchmark --quality

# One language, machine-readable
neuralmind benchmark --quality --suite go --json

# Compare against the committed measured baseline (reports metric deltas)
neuralmind benchmark --quality --baseline evals/quality/baseline.json

# Dependency-free validation of the suites + metric math (no embeddings)
python -m evals.quality.runner --selfcheck

Sample (markdown) output — measured on the committed fixtures:

## NeuralMind retrieval-quality eval

| Suite | Queries | MRR | Answerability | Recall@5 | Precision@5 | Gate |
|-------|--------:|----:|--------------:|---------:|------------:|:----:|
| `go`         | 10 | 0.950 | 100% | 0.833 | 0.603 | PASS |
| `python`     | 10 | 0.900 | 100% | 0.833 | 0.612 | PASS |
| `typescript` | 10 | 0.900 | 100% | 0.800 | 0.562 | PASS |

**Overall: PASS**

The exit code is non-zero if any suite drops below the floors in evals/quality/harness.py (DEFAULT_THRESHOLDS), so CI can gate on it. The measured baseline lives at evals/quality/baseline.json; the self-benchmark workflow runs this on every PR (where real embeddings are available) and posts the table + baseline deltas as a PR comment.

Sample Output

=== NeuralMind Benchmark ===

Project: MyApp
Total Nodes: 241
Communities: 93
Estimated Full Codebase: 50,000 tokens

| Query Type | Tokens | Reduction | Latency |
|------------|--------|-----------|----------|
| Wake-up context | 341 | 146.6x | 45ms |
| How does authentication work? | 739 | 67.7x | 187ms |
| What are the main API endpoints? | 748 | 66.8x | 192ms |
| Explain the database models | 812 | 61.6x | 201ms |
|------------|--------|-----------|----------|
| **Average** | **660** | **85.7x** | **156ms** |

---
Benchmark completed in 625ms

stats

Show statistics about the neural index.

neuralmind stats <project_path> [OPTIONS]

Arguments

Argument	Required	Description
`project_path`	Yes	Path to project root

Options

Option	Default	Description
`--json`, `-j`	False	Output as JSON

Output

Displays:

Node counts by type
Community statistics
Embedding information
Index storage size
Last build timestamp

Examples

# Basic stats
neuralmind stats /path/to/project

# JSON format
neuralmind stats /path/to/project --json

Sample Output

=== NeuralMind Statistics ===

Project: MyApp
Graph Path: /path/to/project/graphify-out/graph.json
DB Path: /path/to/project/graphify-out/neuralmind_db

## Index Summary
- Total Nodes: 241
- Total Edges: 203
- Communities: 93
- Embedding Dimensions: 384

## Node Types
- Functions: 142 (58.9%)
- Classes: 45 (18.7%)
- Files: 38 (15.8%)
- Database Models: 16 (6.6%)

## Storage
- Index Size: 12.4 MB
- Cache Size: 2.1 MB

## Build Info
- Last Build: 2024-01-15 14:30:22
- Build Duration: 8.3s
- Embedding Model: all-MiniLM-L6-v2

validate (v0.23.0+)

Validate the project’s canonical intermediate representation (IR) — the versioned, producer-agnostic contract NeuralMind builds from graph.json. Runs a static schema check; no vector backend required (it never touches ChromaDB/turbovec).

neuralmind validate [project_path] [OPTIONS]

Arguments

Argument	Required	Description
`project_path`	No (default `.`)	Path to project root

Options

Option	Default	Description
`--write`	False	(Re)materialize the IR to `.neuralmind/index_ir.json` — the in-place migration path for a legacy project that predates the IR (no rebuild).
`--json`, `-j`	False	Output a machine-readable summary (for CI/dashboards)

What it checks

errors (exit code 1): dangling edge endpoints, missing endpoints, duplicate node ids, malformed synapse endpoints, unsupported (too-new) ir_version.
warnings: orphaned (edgeless) nodes, unknown node kinds, unknown edge relations, and stale synapses (learned memory pointing at nodes a rebuild removed) — forward-compatibility / hygiene signals.

It also reports the IR contract version, source backend + producer schema version, coverage (coarse/precise), per-kind / per-language counts, and the learned-synapse count (folded in backend-free from the SQLite store).

Examples

# Validate the IR for the current project
neuralmind validate .

# Machine-readable summary
neuralmind validate . --json

# Migrate a legacy project's state to the IR in place (no rebuild)
neuralmind validate . --write

Sample Output

IR version:      1
Source backend:  neuralmind.graphgen (tree-sitter)
Source schema:   v1
Coverage:        coarse
Entities:        135 nodes, 185 edges, 18 clusters
Node kinds:      document=56, file=13, function=41, symbol=25
Languages:       python=135
------------------------------------------------------------
VALID — 0 errors, 0 warning(s).

function is inferred from the built-in backend’s call-form labels (name()); a producer that doesn’t follow that convention maps those to the generic symbol. Learned synapses, when a .neuralmind/synapses.db exists, are folded in and shown in the --json synapses count.

The IR is also exposed as a public Python API: from neuralmind import IndexIR, from_graph_json, validate_ir, validate_project.

doctor (v0.12.0+)

Diagnose a project’s NeuralMind setup and print an actionable fix for anything that isn’t wired up. Read-only — it never builds or mutates state.

neuralmind doctor [project_path] [--json]

Arguments:

Argument	Required	Default	Description
`project_path`	No	`.`	Project root to inspect
`--json`, `-j`	No	`false`	Emit machine-readable JSON

Checks: code graph, semantic index, backend (v0.22.0+), synapse memory, MCP server, Claude Code hooks, and query-memory consent. Each reports ok, warn (optional/learned-over-time), or fail (setup incomplete). The Backend check reports the configured value (e.g. auto), what it resolves to (turbovec or chroma), and whether the turbovec stack is installed — so the per-environment default is never a silent mystery.

Exit codes: 0 when no check failed (warnings allowed), 1 when any check failed — so you can gate a CI step or an agent’s provisioning on neuralmind doctor.

Example:

neuralmind doctor .

NeuralMind doctor — /path/to/project
============================================================
  [ ok ] Code graph: 1240 nodes at /path/to/project/graphify-out/graph.json
  [ ok ] Semantic index: 1240 nodes embedded (chromadb backend)
  [ ok ] Backend: turbovec (auto-selected; turbovec stack available)
  [warn] Synapse memory: no synapses.db yet (nothing learned)
         -> It populates automatically as you query and edit the codebase.
  [ ok ] MCP server: MCP SDK importable (neuralmind-mcp ready)
  [warn] Claude Code hooks: not installed
         -> Install them: neuralmind install-hooks
  [ ok ] Query memory: enabled (logging queries for learning)
============================================================

JSON output (--json) is stable for scripting and agent consumption:

{
  "status": "fail",
  "checks": [
    {"name": "Code graph", "status": "fail",
     "detail": "not found at /repo/graphify-out/graph.json",
     "fix": "Generate it: neuralmind build /repo"}
  ]
}

eval (v0.14.0+)

Run the faithfulness eval: does NeuralMind’s selected context contain more gold facts than a matched-budget naive baseline? It self-evaluates against the committed reference fixture + gold-fact set (which ship with the source repository), so — like neuralmind benchmark — it’s a quality self-test, not a per-repo command.

neuralmind eval [project_path] [--json] [--selfcheck] [--onboarding]

Arguments:

Argument	Required	Default	Description
`project_path`	No	the gold-set fixture	Project to evaluate
`--json`, `-j`	No	`false`	Emit the report as JSON
`--selfcheck`	No	`false`	Validate the gold set + offline scorer only (no retrieval deps)
`--onboarding`	No	`false`	Run the onboarding-lift eval instead — committed team memory vs a cold agent (see `evals/onboarding/`)

What it reports: the faithfulness delta — mean expected-fact recall of NeuralMind’s context minus the naive baseline’s, at a matched per-query token budget — plus grounding rate, contradiction rate, and a per-query breakdown. A positive delta means smart selection beats dumb truncation at equal token cost. The default judge is 100% offline; an opt-in LLM-as-judge sits behind NEURALMIND_EVAL_LLM_JUDGE=1 and is never the default or the CI gate.

What --onboarding reports: the onboarding lift — onboarded − cold top-k module hit-rate (the share of a query’s expected modules that land in the ranked top-k retrieval the agent sees), the slice associative recall re-ranks within. Fact-recall and full-context grounding print as honest secondaries: at a fixed budget fact-recall is budget-traded (slightly negative on the tiny fixture) and grounding saturates, so neither is the gated headline. It’s the same top-k hit-rate signal as the self-benchmark’s Phase-3 A/B.

Requirements: the A/B needs the retrieval stack (chromadb) and a built index; without them it degrades with an actionable message. --selfcheck needs neither. From an installed wheel (where the evals/ package isn’t bundled), run it from a source checkout instead: python -m evals.faithfulness.runner --run.

learn (deprecated, v0.25.0)

Deprecated and a no-op since v0.25.0. The learned_patterns cooccurrence reranker this command used to populate was removed. The command now prints a deprecation notice and exits 0, so existing scripts and CI that call it keep working unchanged.

neuralmind learn <project_path>   # prints a deprecation notice, exits 0

Learning is now handled entirely by the synapse layer, which learns continuously and automatically from queries, edits, and tool calls — no manual step, and edges decay instead of going stale. A 2×2 A/B on the benchmark fixture showed the old reranker added 0.0 points to top-k hit rate while the synapse layer alone adds +11.6 points.

To see what’s been learned, use neuralmind stats or neuralmind memory inspect. For the full rationale and migration notes, see the v0.25.0 release notes.

next (v0.11.0+)

Predict what typically follows a node (file path or node id) in the learned directional transition graph. Pairs with the record_sequence calls the file watcher runs automatically on every batched flush.

neuralmind next <project_path> <from_node> [--n 5] [--namespace NAME] [--json]

Arguments

Argument	Required	Description
`project_path`	Yes	Path to project root
`from_node`	Yes	Source node — usually a file path; can be any string the transition recorder has seen

Options

Option	Default	Description
`--n`	`5`	Top-N successors to return
`--namespace`	merged	(v0.24.0+) Read one memory namespace at raw weights (e.g. `branch:feature-x`). Default is the merged view: active namespace 1.0× + `personal` 0.8× + `shared` 0.5×
`--json`, `-j`	False	Output as JSON

Examples

# What do I usually edit after the auth handlers?
neuralmind next . src/auth/handlers.py

# JSON for scripting
neuralmind next . src/auth/handlers.py --n 10 --json

Sample output:

After src/auth/handlers.py:
2%  tests/test_auth.py
4%  src/auth/middleware.py
1%  docs/auth.md
3%  src/auth/__init__.py
0%  src/main.py

The same capability is exposed via MCP as neuralmind_next_likely and via Python as SynapseStore.next_likely(from_node, top_k=5). The file watcher must have been running at some point for this to return results — fresh installs need a few sessions before the transition graph accumulates signal.

memory (v0.24.0+)

Namespace-level controls over the learned synapse memory (PRD 4). Every learned association carries a namespace — personal (default; all pre-v0.24 memory migrates here losslessly), shared (imported team baseline), branch:<name> (per-git-branch, detected automatically), and ephemeral (session scratch, cleared at session boundaries). All four subcommands work without a built index — the store is stdlib SQLite.

neuralmind memory inspect [project_path] [--namespace NAME] [--json]
neuralmind memory reset   [project_path] --namespace NAME [--json]
neuralmind memory export  [project_path] [--namespace NAME] [-o FILE]
neuralmind memory import  <file> [--project-path PATH] [--namespace NAME] [--json]

Subcommands

Subcommand	What it does
`inspect`	Contribution by namespace — edges, total weight, transitions, nodes — plus the active namespace and schema version. Also folded into `neuralmind stats`.
`reset`	Clear one namespace (`--namespace` is required). The project index and every other namespace are untouched — the surgical alternative to a full retrain.
`export`	Write one namespace as a portable, versioned JSON bundle reusing the IR’s `IRSynapse` shape (the PRD 8 team-memory on-ramp). Defaults to the active namespace; `-o` writes a file, otherwise stdout.
`import`	Validate a bundle (format + version + entries) and merge it into a target namespace (default: the bundle’s own). Merging keeps the MAX of weight/count per edge, so re-importing the same bundle is idempotent. A malformed bundle is rejected wholesale — never partially imported.

Examples

# What has the agent learned, and where does it live?
neuralmind memory inspect .

# A feature branch merged — drop exactly its memory
neuralmind memory reset . --namespace branch:feature-x

# Ship a team baseline to a new teammate
neuralmind memory export . --namespace personal -o team-baseline.json
neuralmind memory import team-baseline.json --namespace shared

How the active namespace is resolved

NEURALMIND_NAMESPACE env var → memory_namespace: in neuralmind-backend.yaml → branch:<name> when the repo is on a non-default git branch (best-effort git rev-parse, 3s timeout) → personal. A non-repo, detached HEAD, or missing git all degrade safely to personal. Long-lived processes (the daemon, the MCP server) detect a git checkout between writes via a cheap .git/HEAD fingerprint and re-resolve automatically — no restart needed.

Merged-read weighting

Recall, next, and stats default to a merged view with explicit, published constants (neuralmind/synapses.py):

merged_weight = 1.0 × active  +  0.8 × personal  +  0.5 × shared
                (W_BRANCH)       (W_PERSONAL)        (W_SHARED)

On the default branch the active namespace is personal (read at 1.0×), so behavior is identical to pre-namespace releases. Per-namespace decay: shared is sticky, personal/branch:* decay at the standard rates, ephemeral fades fast with no LTP floor. Traced queries (query --trace) attribute each synapse boost to its namespace via namespace_contribution.

skeleton

Print a compact graph-backed view of a file — functions, rationales, and call graph — without loading the full source.

neuralmind skeleton <file_path> [--project-path .] [--json]

Arguments

Argument	Required	Description
`file_path`	Yes	Path to the source file (absolute or project-relative)

Options

Option	Default	Description
`--project-path`	`.`	Project root directory
`--json`, `-j`	False	Output as JSON

Examples

# Skeleton for a file in the current project
neuralmind skeleton src/auth/handlers.py

# Skeleton with explicit project root
neuralmind skeleton src/auth/handlers.py --project-path /path/to/project

# JSON output
neuralmind skeleton src/auth/handlers.py --json

last (v0.10.0+)

Print the most recent Bash output the PostToolUse hook cached, so an agent can recover the dropped middle without re-running the command.

Every time the compress-bash hook fires, it stashes the raw pre-compression stdout/stderr to <project>/.neuralmind/last_output.json (single-slot, 2 MB cap, atomic temp-file + rename writes). neuralmind last surfaces it.

neuralmind last [project_path] [--json]

Arguments

Argument	Required	Description
`project_path`	No	Project root containing `.neuralmind/last_output.json` (default: current directory)
`--json`, `-j`	No	Emit the full payload as JSON (timestamp, command, exit code, stdout, stderr)

Examples

# Human-readable: what the agent would have seen pre-compression.
neuralmind last

# Full JSON payload — useful for scripted recovery flows.
neuralmind last --json

# When no cache exists yet (no Bash call has fired the hook).
neuralmind last
# → "No cached output found at <path>. Run a Bash tool call through Claude Code first…"
# → exits with status 1

Exit codes

Code	Meaning
`0`	Cache present and printed
`1`	No cache exists (no recent Bash call)

When to use

Scenario	Recovery cost without `last`	With `last`
Inspecting compressed `npm test` middle	Re-run (~28s)	Free lookup
Reading dropped log lines from a non-deterministic API call	Re-run + likely different output	Free lookup, identical bytes
Reading dropped output from a destructive command	Re-run impossible	Free lookup

install-hooks

Install or uninstall Claude Code lifecycle hooks. As of v0.4.0 this registers four event blocks (idempotent — re-running only updates the NeuralMind block, leaving any user hooks untouched):

Event	What runs	Purpose
`PostToolUse`	Read/Bash/Grep compressors	Token reduction on tool output
`SessionStart` (v0.4.0)	`synapse decay()` + memory export	Age unused synapses; surface learned associations to Claude Code’s auto-memory
`UserPromptSubmit` (v0.4.0)	Spreading activation from prompt	Inject ranked synapse neighbors as `additionalContext`
`PreCompact` (v0.4.0)	`normalize_hubs()`	Prevent runaway hub nodes before context compaction

neuralmind install-hooks [project_path] [--global] [--uninstall]

Arguments

Argument	Required	Description
`project_path`	No	Project root (default: current directory). Ignored when `--global` is set

Options

Option	Default	Description
`--global`	False	Install hooks in `~/.claude/settings.json` (all projects)
`--uninstall`	False	Remove NeuralMind hooks while preserving other tools’ hooks

Examples

# Install hooks for current project
neuralmind install-hooks .

# Install hooks globally
neuralmind install-hooks --global

# Uninstall project hooks
neuralmind install-hooks --uninstall

# Uninstall global hooks
neuralmind install-hooks --uninstall --global

Bypass temporarily:

NEURALMIND_BYPASS=1 claude-code ...

install-mcp (v0.19.0+)

Register the NeuralMind MCP server (neuralmind-mcp) with one or more AI coding agents. Auto-detects installed clients and merges a neuralmind entry into each client’s mcpServers config without clobbering your other servers (idempotent — re-running is a no-op).

neuralmind install-mcp [project_path] [--client NAME] [--all] [--print]

Clients & config locations

Client	Scope	Config file
`claude-code` (default)	project	`.mcp.json`
`cursor`	project	`.cursor/mcp.json`
`claude-desktop`	user	platform `claude_desktop_config.json`
`cline`	user	VS Code `cline_mcp_settings.json`

Options

Option	Default	Description
`--client`	`claude-code`	Which single client to register with
`--all`	False	Register with every detected client (auto-detection)
`--print`	False	Print the config snippet to paste manually; write nothing

Examples

# Register with Claude Code for this project (writes .mcp.json)
neuralmind install-mcp

# Register with every agent installed on this machine/project
neuralmind install-mcp --all

# A specific client
neuralmind install-mcp --client cursor

# Just show me the snippet
neuralmind install-mcp --print

Restart the client after registering so it picks up the new server. The agent then exposes NeuralMind’s MCP tools (wakeup, query, search, skeleton, build, stats, …).

init-hook

Install (or update) a Git post-commit hook that rebuilds the neural index automatically after every commit. Safe and idempotent — re-running only updates the NeuralMind block without touching other hooks.

neuralmind init-hook [project_path]

Arguments

Argument	Required	Description
`project_path`	No	Project root (default: current directory)

Examples

# Install hook in current project
neuralmind init-hook .

# Install hook for a specific project
neuralmind init-hook /path/to/project

watch (v0.4.0+)

Run the file activity → synapse co-activation daemon in the foreground. Edits to project files are debounced into batches and fed into the synapse store, so the v0.4.0 brain-like layer keeps learning even when no query runs. Periodic decay ticks age unused weights without manual intervention. Stops cleanly on Ctrl-C.

neuralmind watch [project_path] [--debounce SECONDS] [--decay-interval SECONDS] [--quiet] [--reindex]

Arguments

Argument	Required	Description
`project_path`	No	Project root (default: current directory)

Flags

Flag	Default	Description
`--debounce`	`0.75`	Seconds to coalesce rapid edits into one co-activation batch
`--decay-interval`	`600`	Seconds between decay ticks; `0` disables periodic decay
`--quiet`	off	Suppress per-batch logging (still prints final summary on stop)
`--reindex`	off	(v0.18.0+) Incrementally re-index edited files into the built-in graph as they change — re-parses just those files and re-embeds only their nodes (unchanged files are skipped). Built-in backend only; needs the retrieval stack in the watch process.

Examples

# Always-on learning for the current project
neuralmind watch &

# Background it and only log the final summary
neuralmind watch /path/to/repo --quiet &

# Disable periodic decay (decay only runs from SessionStart hook)
neuralmind watch . --decay-interval 0

# Keep the index live as you edit (incremental re-index, v0.18.0+)
neuralmind watch . --reindex

Notes

Backed by watchdog when present, with a polling fallback when not. No mandatory new dependency.
Pairs with neuralmind install-hooks — the watcher learns from edits, the lifecycle hooks learn from queries and tool calls, and the same <project>/.neuralmind/synapses.db store is the single source of truth.
For “always on” across reboots, wrap in systemd, launchd, or tmux. NeuralMind deliberately doesn’t self-daemonize.

serve (v0.5.4; live feed v0.6.0+)

Start the graph-view UI — a local, dependency-free, Obsidian-style force-directed graph over the same index and synapse store your AI agent queries. v0.6.0 made the canvas live: synapse + file events stream to the browser over SSE, affected nodes pulse, a sidebar log shows recent events. Stops cleanly on Ctrl-C.

The server binds to 127.0.0.1 by default and prints a per-session auth-token URL on startup; pass that URL to the browser so untrusted local processes can’t read your graph.

neuralmind serve [project_path] [--port PORT] [--no-browser] [--editor EDITOR] [--no-auth]

Arguments

Argument	Required	Description
`project_path`	No	Project root (default: current directory)

Flags

Flag	Default	Description
`--port`	`8765`	TCP port to bind to
`--no-browser`	off	Don’t auto-open a browser tab on startup
`--editor`	`$EDITOR`	Editor command used by the “Open in editor” button — `code`, `code -n`, `cursor`, `vim`, `subl`, `idea`, etc.
`--no-auth`	off	Disable the per-session auth token. Only use on a trusted host.

Examples

# Run against the current project
neuralmind serve .

# Custom editor for the "open in editor" button
neuralmind serve . --editor "code -n"

# Pick a different port and skip the browser
neuralmind serve . --port 9000 --no-browser

# Skip auth for a kiosk / trusted local host
neuralmind serve . --no-auth

Live activity feed (v0.6.0+)

The canvas updates in real time as the brain works:

Synapse events — every SynapseStore.reinforce() call publishes a synapse event over the in-process event bus; the affected pair of nodes pulse on the canvas.
File activity events — every coalesced edit batch from the neuralmind watch daemon (or from Claude Code’s PostToolUse hooks) publishes a file_activity event; affected nodes pulse.
Sidebar log — the most recent ~80 events render as a scrolling feed with timestamps. Click an entry to focus the corresponding node on the canvas.

Cross-process activity bridge (v0.6.0+)

When serve and the activity source live in different processes — a separate neuralmind watch daemon, a Claude Code session — each event_bus.publish() call also appends a JSON line to <project>/.neuralmind/events.jsonl. The serve process tails that file in a background thread and re-emits anything it didn’t originate. Net result: one canvas, all processes, no IPC complexity.

Behaviour:

NEURALMIND_EVENT_LOG=0 disables the writer (in-process feed still works).
The tailer is best-effort. If the file disappears or rolls, the next event re-creates it.
The bus stays the primary path. The JSONL is a fallback, not a queue.

Notes

Read-only over HTTP. Edits to nodes/synapses still go through the regular CLI and MCP tools; the UI only inspects.
The /api/open endpoint launches $EDITOR against an allowlist pre-computed from the graph’s source_file set, so a tampered client can’t trick the server into opening arbitrary paths.
All assets in neuralmind/web/ (HTML, JS, CSS) are read-only at runtime; the server doesn’t generate any of them.
Graph payload is cached per-session in _Handler._graph_cache; any endpoint touching graph state respects _graph_lock.
Vanilla-JS frontend, stdlib-only HTTP server, no CDN. Safe to run behind a firewall.

daemon (v0.23.0+)

Manage the local NeuralMind daemon (experimental — PRD 5). The daemon holds each project’s state warm so repeated queries skip cold backend init. CLI read commands (query, stats) prefer it automatically when it’s running and fall back to direct mode otherwise.

neuralmind daemon {start|stop|restart|status} [OPTIONS]

Actions

Action	Description
`start`	Launch the daemon in the background (writes a discovery file). No-op if already running.
`stop`	Ask the running daemon to shut down gracefully; clears stale discovery.
`restart`	Stop (if running) then start.
`status`	Show pid, uptime, warm projects, and active jobs (exit 3 if not running).

Options

Option	Default	Description
`--host`	`127.0.0.1`	Host to bind (loopback)
`--port`	`8787`	Port to bind
`--foreground`	False	Run in the foreground instead of detaching (`start`/`restart`)
`--json`, `-j`	False	Machine-readable `status` output

Behavior

One per-user daemon, many projects. A project registry initializes each NeuralMind once and reuses it; a per-project lock serializes build/query/watch so they can’t corrupt the index or synapse store; slow builds run as background jobs.
Auto-preference + fallback. neuralmind query / stats use the daemon when reachable (output marked via: daemon in --json), else run directly. Force direct mode with NEURALMIND_NO_DAEMON=1.
Crash-safe discovery. A stale discovery file (dead pid / unreachable) is cleaned up automatically, so a crashed daemon never wedges the CLI.
Shared API. The daemon speaks one transport-agnostic contract (health / status / query / search / stats / build / validate / jobs); the neuralmind-daemon console script runs it directly. Token-guarded even on loopback.

# Warm daemon, then fast repeat queries
neuralmind daemon start
neuralmind query . "how does auth work?"   # served warm (via: daemon)
neuralmind daemon status --json
neuralmind daemon stop

Exit Codes

Code	Meaning
0	Success
1	General error
2	Invalid arguments
3	graph.json not found
4	Index not built (run `build` first)
5	Database error

Environment Variables

Variable	Default	Description
`NEURALMIND_MEMORY`	`1`	Set to `0` to disable query memory logging
`NEURALMIND_LEARNING`	`1`	(deprecated, v0.25.0) Formerly disabled the `learned_patterns` cooccurrence reranker, which was removed in v0.25.0. Now inert — recognized but ignored. To disable the synapse layer’s prompt-time recall, use `NEURALMIND_SYNAPSE_INJECT=0`.
`NEURALMIND_BYPASS`	unset	Set to `1` to bypass PostToolUse hook compression temporarily
`NEURALMIND_SYNAPSE_INJECT`	`1`	(v0.4.0+) Set to `0` to disable spreading-activation context injection in the `UserPromptSubmit` hook
`NEURALMIND_SYNAPSE_EXPORT`	`1`	(v0.4.0+) Set to `0` to disable session-start synapse memory export
`NEURALMIND_EVENT_LOG`	`1`	(v0.6.0+) Set to `0` to disable the cross-process JSONL event-bridge writer at `<project>/.neuralmind/events.jsonl`. The in-process event bus is unaffected; `serve` running in the same process as the activity source still gets a live feed.
`NEURALMIND_OUTPUT_CACHE`	`1`	(v0.10.0+) Set to `0` to disable the recovery cache that backs `neuralmind last`.
`NEURALMIND_OUTPUT_CACHE_MAX`	`2097152`	(v0.10.0+) Total size cap (bytes) for the recovery cache. Oversize payloads are split proportionally between stdout/stderr and truncated keeping head + tail.
`NEURALMIND_BASH_SMALL`	`500`	(v0.10.0+) Threshold below which failing Bash outputs pass through verbatim (no compression marker). Tunable to suit your noise tolerance.
`NEURALMIND_BASH_MAX_CHARS`	`3000`	Threshold above which successful Bash outputs get compressed.
`NEURALMIND_BASH_TAIL`	`3`	Number of tail lines always kept verbatim in compressed Bash output.
`NEURALMIND_EVAL_LLM_JUDGE`	`0`	(v0.13.0+) Opt-in LLM-as-judge mode for the offline faithfulness eval harness (`evals/faithfulness/`). Off by default and never the CI gate; when set, the runner prints a notice that answers + gold facts would be sent to a third-party API. The default judge is the zero-network offline expected-fact-recall scorer.
`NEURALMIND_PARITY_REDUCTION_TOL`	`0.25`	(v0.15.0+) Backend parity gate (`evals/parity/run.py`): max fraction the built-in backend’s mean token reduction may sit below graphify’s (0.25 = within 25%).
`NEURALMIND_PARITY_FAITHFULNESS_TOL`	`0.10`	(v0.15.0+) Backend parity gate: max absolute points the built-in backend’s faithfulness delta / fact recall may sit below graphify’s (0.10 = 10 points).
`NEURALMIND_PARITY_REDUCTION_FLOOR`	`4.0`	(v0.15.0+) Backend parity gate: absolute minimum mean reduction the built-in backend must clear, independent of graphify (mirrors the self-benchmark floor).
`NEURALMIND_PARITY_FAITHFULNESS_FLOOR`	`0.0`	(v0.15.0+) Backend parity gate: absolute minimum faithfulness delta the built-in backend must clear (mirrors the eval gate — smart selection ≥ matched-budget naive truncation).
`NEURALMIND_PARITY_COVERAGE_FLOOR`	`0.90`	(v0.16.0+) Backend parity gate: minimum fraction of graphify’s per-language symbols the built-in backend must recover for TypeScript/Go (structural parity, since no gold-fact set exists for those fixtures yet).
`NEURALMIND_PRECISION`	unset	(v0.17.0+) Set to `1` to enable the optional SCIP precision pass: when a `*.scip` index is present in the project root, the built-in backend’s heuristic `calls`/`inherits` edges are replaced with compiler-accurate ones for the files the index covers. Off by default; a no-op when unset or when no index is found.
`NEURALMIND_ONNX_MODEL_DIR`	unset	(v0.21.0+) Path to a pre-extracted `all-MiniLM-L6-v2` ONNX folder (`model.onnx` + `tokenizer.json`) for the ChromaDB-free `turbovec` backend’s bundled embedder. When unset, the model is resolved from NeuralMind’s cache, an existing ChromaDB cache, or downloaded (SHA256-verified). Set it for air-gapped installs so no network is needed.
`NEURALMIND_NO_DAEMON`	unset	(v0.23.0+) Set to `1` to force CLI commands to run in direct mode even when a daemon is running (skips the daemon auto-preference for `query`/`stats`).
`NEURALMIND_NAMESPACE`	unset	(v0.24.0+) Pin the active memory namespace for this process (e.g. `ephemeral` for throwaway exploration, `shared` on a CI box building team baseline). Overrides config and git-branch detection. Resolution order: this var → `memory_namespace:` in `neuralmind-backend.yaml` → `branch:<name>` on a non-default git branch → `personal`.
`NEURALMIND_DAEMON_HOME`	unset	(v0.23.0+) Override the directory holding the daemon discovery file (`daemon.json`). Defaults to `~/.neuralmind`. Mainly for tests / running an isolated daemon.

Vector backend selection (v0.21.0+)

NeuralMind’s vector store is pluggable. As of v0.22.0 the default is auto (an unset config behaves the same): it resolves to the ChromaDB-free turbovec backend when its stack (turbovec + onnxruntime + tokenizers) is importable, and otherwise falls back to chroma. A plain pip install neuralmind (no [turbovec] extra) therefore still resolves to ChromaDB — nothing changes — while installs that added the extra get the ChromaDB-free path automatically.

To pin a backend explicitly (an explicit value always wins over auto), drop a neuralmind-backend.yaml at the project root:

backend: turbovec   # force the ChromaDB-free path: TurboVec ANN + bundled OnnxMiniLMEmbedder
# backend: graph    # force ChromaDB (alias: chroma)
# backend: auto     # the default — turbovec when its deps are installed, else chroma

Install the extra: pip install "neuralmind[turbovec]" (pulls turbovec, onnxruntime, tokenizers, numpy). Vectors are byte-identical to the chroma backend’s, so retrieval quality is at/above parity; the index is 8–16× smaller. Accepted values: auto (default), graph / chroma, turbovec, in_memory (offline tests).

One-time auto-reindex. When auto resolves to turbovec for a project that still has a legacy ChromaDB index and no turbovec index yet, the next build reindexes from graph.json and prints a one-line notice. The old ChromaDB index is left in place as a fallback — nothing is deleted.

Run neuralmind doctor to see which backend the current environment resolves to (see the Backend line).

Examples

Complete Workflow

# 1. Build neural index (the code graph is generated automatically)
neuralmind build ~/projects/myapp

# 3. View statistics
neuralmind stats ~/projects/myapp

# 4. Get wake-up context for new conversation
neuralmind wakeup ~/projects/myapp > context.md

# 5. Query specific functionality
neuralmind query ~/projects/myapp "How does the payment system work?"

# 6. Search for specific entities
neuralmind search ~/projects/myapp "PaymentController" --n 5

# 7. Run benchmark
neuralmind benchmark ~/projects/myapp

Scripting Integration

#!/bin/bash
# update_and_query.sh - Update index and run queries

PROJECT="$1"
QUERY="$2"

# Rebuild if graph changed
if [ graphify-out/graph.json -nt graphify-out/neuralmind_db ]; then
    echo "Graph updated, rebuilding index..."
    neuralmind build "$PROJECT"
fi

# Run query
neuralmind query "$PROJECT" "$QUERY" --json

Piping to AI Tools

# Get context and pipe to clipboard (macOS)
neuralmind wakeup ~/projects/myapp | pbcopy

# Get context and pipe to clipboard (Linux)
neuralmind wakeup ~/projects/myapp | xclip -selection clipboard

# Save context to file for AI assistant
neuralmind query ~/projects/myapp "Explain the auth system" > auth_context.md

neuralmind

CLI Reference

Table of Contents

Overview

Getting Help

Global Options

Commands

build

Arguments

Options

Output

Examples

Prerequisites

query

Arguments

Options

Output

Retrieval traces (v0.23.0+)

Examples

Sample Output

wakeup

Arguments

Options

Output

Examples

Sample Output

search

Arguments

Options

Output

Examples

Sample Output

benchmark

Arguments

Options

Output

Examples

Quality-eval mode (v0.23.0+)

Sample Output

stats

Arguments

Options

Output

Examples

Sample Output

validate (v0.23.0+)

Arguments

Options

What it checks

Examples

Sample Output

doctor (v0.12.0+)

eval (v0.14.0+)

learn (deprecated, v0.25.0)

next (v0.11.0+)

Arguments

Options

Examples

memory (v0.24.0+)

Subcommands

Examples

How the active namespace is resolved

Merged-read weighting

skeleton

Arguments

Options

Examples

last (v0.10.0+)

Arguments

Examples

Exit codes

When to use

install-hooks

Arguments

Options

Examples

install-mcp (v0.19.0+)

Clients & config locations

Options

Examples