🧠 NeuralMind

Semantic code intelligence for AI coding agents — smart context retrieval + tool-output compression in one package.

NeuralMind turns a code repository into a queryable neural index. AI agents use it to answer code questions in ~800 tokens instead of loading 50,000+ tokens of raw source.

⚖️ Not affiliated with NeuralMind.ai. This project is an independent, open-source tool for semantic code intelligence.

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🔒 Security & Compliance

For enterprises and regulated industries:

• 100% Local Processing – Your code never leaves your machine. All embeddings are generated and stored locally using ChromaDB.
• No External APIs – NeuralMind runs completely offline. No cloud services, no telemetry, no data exfiltration.
• Explainable AI – Every context decision is auditable. Know exactly which code was retrieved (Extracted) vs. inferred by the model.
• Open-Source & MIT Licensed – Full transparency. No hidden clauses, no vendor lock-in. Audit the code yourself.
• GDPR/HIPAA-Friendly – Process sensitive code without compliance concerns. All data stays under your control.

For CTOs & Security Teams:

• ✅ Zero external dependencies for code storage
• ✅ Runs behind your firewall or on-premise
• ✅ No collection of usage metrics or code patterns
• ✅ Predictable, reproducible results (not a black box)
• ✅ Works with proprietary and sensitive code

See full security policy

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📌 For AI Coding Agents

If you are Claude Code, Codex, Cursor, Cline, or any AI agent with NeuralMind installed, start here.

Check if NeuralMind is active

neuralmind stats .

Expected output when ready:

Project: your-project
Built: True
Nodes: 241

If Built: False, run graphify update . && neuralmind build . first.

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Startup workflow

Every new session, do this first:

neuralmind wakeup .

Or via MCP:

neuralmind_wakeup(project_path=".")

This returns ~365–600 tokens of structured project context:

• Project name and description (from CLAUDE.md, mempalace.yaml, or README.md first line)
• How many code entities and clusters are indexed
• Architecture overview: top 10 code clusters with their entity types and sample names
• Sections from graphify-out/GRAPH_REPORT.md if present

Use this output as your orientation before writing any code. It replaces reading the entire repository.

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Decision tree — which tool to call

Need to understand the project?
  └─► neuralmind wakeup .               (MCP: neuralmind_wakeup)      ~400 tokens

Answering a specific code question?
  └─► neuralmind query . "question"     (MCP: neuralmind_query)       ~800–1100 tokens

About to open a source file?
  └─► neuralmind skeleton <file>        (MCP: neuralmind_skeleton)    ~5–15× cheaper than Read
      → Only fall back to Read when you need the actual implementation body
      → Use NEURALMIND_BYPASS=1 when you truly need raw source

Searching for a specific function/class/entity?
  └─► neuralmind search . "term"        (MCP: neuralmind_search)      ranked by semantic similarity

Made code changes and need to update the index?
  └─► neuralmind build .                (MCP: neuralmind_build)       incremental — only re-embeds changed nodes

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Understanding the output

wakeup / query output format

## Project: myapp

Full-stack web app for task management. Uses React 18, Node.js, and PostgreSQL.

Knowledge Graph: 241 entities, 23 clusters
Type: Code repository with semantic indexing

## Architecture Overview

### Code Clusters
- Cluster 5 (45 entities): function — authenticate_user, hash_password, verify_token
- Cluster 12 (23 entities): class — UserController, AuthMiddleware, SessionStore
- Cluster 3 (18 entities): function — createTask, updateTask, deleteTask
...

## Relevant Code Areas        ← query only; absent from wakeup
### Cluster 5 (relevance: 1.73)
Contains: function entities
- authenticate_user (code) — auth.py
- verify_token (code) — auth.py

## Search Results             ← query only
- AuthMiddleware (score: 0.91) — middleware.py
- jwt_handler (score: 0.85) — auth/jwt.py

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

Layer meanings:

Layer	Name	Always loaded	Content
L0	Identity	✅ yes	Project name, description, graph size
L1	Summary	✅ yes	Architecture, top clusters, GRAPH_REPORT sections
L2	On-demand	query only	Top 3 clusters most relevant to the query
L3	Search	query only	Semantic search hits (up to 10)

skeleton output format

# src/auth/handlers.py  (community 5, 8 functions)

## Functions
L12   authenticate_user   — Validates credentials and issues JWT
L45   verify_token        — Checks JWT signature and expiry
L78   refresh_token       — Issues new JWT from a valid refresh token
L102  logout              — Revokes refresh token in DB

## Call graph (within this file)
authenticate_user → verify_token, hash_password
refresh_token → verify_token

## Cross-file
verify_token imports_from → utils/jwt.py (high 0.95)
authenticate_user shares_data_with → models/user.py (high 0.91)

[Full source available: Read this file with NEURALMIND_BYPASS=1]

Use skeleton to understand what a file does, how its functions relate, and which other files it depends on — without consuming tokens on the full source body.

search output format

1. authenticate_user (function) - score: 0.92
   File: auth/handlers.py  Community: 5

2. AuthMiddleware (class) - score: 0.87
   File: auth/middleware.py  Community: 5

3. hash_password (function) - score: 0.81
   File: utils/crypto.py  Community: 5

---

PostToolUse hooks — what happens automatically

If neuralmind install-hooks has been run for this project (check for .claude/settings.json), Claude Code automatically compresses tool outputs before you see them:

Tool	What happens	Typical savings
Read	Raw source → graph skeleton (functions, rationales, call graph)	~88%
Bash	Full output → error lines + warning lines + last 3 lines + summary	~91%
Grep	Unlimited matches → capped at 25 + "N more hidden" pointer	varies

This is fully automatic — you do not need to call any extra tools.

To bypass compression for a single command (e.g., when you need the full file body):

NEURALMIND_BYPASS=1 <your command>

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After making code changes

The index does not auto-update unless a git post-commit hook was installed with neuralmind init-hook .. After significant code changes, rebuild manually:

neuralmind build .          # incremental — only re-embeds changed nodes
neuralmind build . --force  # full rebuild — re-embeds everything

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MCP tool quick reference

Tool	When to call	Required params	Returns
neuralmind_wakeup	Session start	project_path	L0+L1 context string, token count
neuralmind_query	Code question	project_path, question	L0–L3 context string, token count, reduction ratio
neuralmind_search	Find entity	project_path, query	List of nodes with scores, file paths
neuralmind_skeleton	Explore file	project_path, file_path	Functions + rationales + call graph + cross-file edges
neuralmind_stats	Check status	project_path	Built status, node count, community count
neuralmind_build	Rebuild index	project_path	Build stats dict
neuralmind_benchmark	Measure savings	project_path	Per-query token counts and reduction ratios

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⚡ Two-phase optimization

┌─────────────────────────────────────────────────────────────┐
│ Phase 1: Retrieval — what to fetch                          │
│   neuralmind wakeup .    →  ~365 tokens (vs 50K raw)        │
│   neuralmind query "?"   →  ~800 tokens (vs 2,700 raw)      │
│   neuralmind_skeleton    →  graph-backed file view          │
├─────────────────────────────────────────────────────────────┤
│ Phase 2: Consumption — what the agent actually sees         │
│   PostToolUse hooks compress Read/Bash/Grep output          │
│   File reads → graph skeleton (~88% reduction)              │
│   Bash output → errors + summary (~91% reduction)           │
│   Search results → capped at 25 matches                     │
└─────────────────────────────────────────────────────────────┘

Combined effect: 5–10× total reduction vs baseline Claude Code.

---

🎯 The Problem

You: "How does authentication work in my codebase?"

❌ Traditional: Load entire codebase → 50,000 tokens → $0.15–$3.75/query
✅ NeuralMind: Smart context → 766 tokens → $0.002–$0.06/query

💰 Real Savings

Model	Without NeuralMind	With NeuralMind	Monthly Savings
Claude 3.5 Sonnet	$450/month	$7/month	$443
GPT-4o	$750/month	$12/month	$738
GPT-4.5	$11,250/month	$180/month	$11,070
Claude Opus	$2,250/month	$36/month	$2,214

Based on 100 queries/day. Pricing sources

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✅ Does it work on your code? Prove it in 5 minutes.

NeuralMind benchmarks itself in CI on every PR. But your codebase isn't our fixture. The only way to know what it does for you is to measure it on your code.

pip install neuralmind graphifyy
cd /path/to/your-project
graphify update . && neuralmind build .
neuralmind benchmark .

You'll get back your actual reduction ratio and per-query token count — typically 30–80× on real repos. No telemetry, nothing uploaded, nothing committed. If the numbers don't justify it, pip uninstall neuralmind and move on — 5 minutes lost.

Want the dollar figure for your team?

neuralmind benchmark . --contribute

That flag produces a ready-to-share JSON blob with your project's numbers, the exact command that produced them, and an estimated monthly savings at your query volume. Paste it into Slack, a design doc, a PR — or optionally contribute it to the public leaderboard.

Full walkthrough: Does NeuralMind work on your codebase?

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🚨 When do I reach for NeuralMind?

Two ways to decide: start with what's annoying you (symptoms), or start with what you're trying to achieve (goals).

Symptoms — "This is happening to me"

What you notice	Reach for	Why it fixes it
Claude Code hits context limits mid-task	neuralmind install-hooks .	Auto-compresses Read/Bash/Grep before the agent sees them (~88–91%)
My monthly LLM bill is climbing	neuralmind query + hooks	40–70× fewer tokens per code question
I start every session re-pasting project structure	neuralmind wakeup .	~400 tokens of orientation; pipe into any chat
Agent reads a 2,000-line file to answer about one function	neuralmind skeleton <file>	Functions + call graph, no body; ~88% cheaper than Read
grep floods the agent with hundreds of matches	neuralmind install-hooks .	Caps at 25 matches with "N more hidden" pointer
The agent is confidently wrong about what my code does	Start session with wakeup; ask with query	Grounds the model in real structure instead of guessing
I want to query my codebase from ChatGPT / Gemini	neuralmind wakeup . | pbcopy	Model-agnostic output; paste into any chat
Retrieval feels random across similar questions	neuralmind learn .	Cooccurrence-based reranking adapts to your patterns
Index feels out of date after a refactor	neuralmind build . (or init-hook once)	Incremental — only re-embeds changed nodes

Goals — "What am I trying to solve for?"

If your goal is…	Do this	Expected outcome
Cut LLM spend on code Q&A	install-hooks + use query for questions	5–10× total reduction vs baseline agent
Faster, more grounded agent responses	wakeup at session start → query / skeleton during	Fewer hallucinations; less re-exploration
Keep all code local (no SaaS, no telemetry)	Default install — no extra config	100% offline; nothing leaves the machine
Work across Claude + GPT + Gemini with one index	Build once, pipe output into any model	Same context quality, model-agnostic
Make retrieval adapt to how your team queries	Enable memory (TTY prompt) + neuralmind learn .	Relevance improves on repeat patterns
Measure savings for a manager or stakeholder	neuralmind benchmark . --json	Per-query tokens, reduction ratios, dollar estimate
Auto-refresh the index as code changes	neuralmind init-hook . (git post-commit)	Every commit rebuilds incrementally

Still not sure?

You probably don't need NeuralMind if:

• Your codebase is under ~5K tokens total (just paste the whole thing in).
• You don't use an AI coding agent.
• You only want inline completions — use Copilot or Cursor directly.

You almost certainly want NeuralMind if any row above describes a recurring frustration, or if your LLM bill has crossed the point where a 40–70× reduction is worth 5 minutes of setup.

See the use-case walkthroughs for step-by-step guides matched to your situation.

---

👤 Who is NeuralMind for?

You are…	NeuralMind gives you…
A Claude Code user watching your token bill climb	PostToolUse compression on every Read/Bash/Grep + ~60× smaller query context
A Cursor user who wants semantic retrieval outside Cursor too	CLI + MCP server that works in any agent with the same index
A Cline / Continue user without a built-in codebase index	Drop-in MCP neuralmind_query and neuralmind_skeleton tools
Running OpenAI / Gemini / local models	Model-agnostic context — pipe wakeup / query output into any chat
A solo developer with a growing monorepo	Incremental rebuilds + learning that adapts to your query patterns
A team tech lead worried about LLM spend	Measurable per-query token reduction with neuralmind benchmark
A security-conscious engineer or in a regulated industry	100% local, offline, no code leaves the machine
A researcher / hobbyist exploring LLM cost optimization	Open-source reference implementation of two-phase token optimization

Not a fit if: you need cross-repo search across a whole organization (use Sourcegraph Cody), or you only want inline completions (use Copilot).

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🏢 Enterprise Use Cases

NeuralMind solves specific pain points for companies at scale:

Regulated Industries (Finance, Healthcare, Legal, Government)

Challenge: AI tools can't be trusted if they can't explain decisions.

NeuralMind Solution:

• Every recommendation is traceable to extracted code (auditable, not guessed)
• Works 100% on-premise — no cloud, no data transfer, zero exfiltration risk
• Meets GDPR, HIPAA, SOC 2, and ISO 27001 requirements
• Explainability by design — see what code fed each decision

Enterprises with Proprietary / Sensitive Code

Challenge: Sending code to external APIs or SaaS models is a legal no-go.

NeuralMind Solution:

• All processing stays on your hardware or internal network
• No ChromaDB cloud — uses local SQLite-compatible storage
• No API keys, no authentication to external vendors
• Process trade secrets, algorithms, and confidential code safely

Large Organizations Scaling AI Coding Assistant Spend

Challenge: 100 developers × Claude Sonnet queries = $50K+/month LLM bill

NeuralMind Solution:

• 40–70× token reduction per query → cut budget by 95%+
• Explicit benchmarking (neuralmind benchmark) to show ROI to finance
• Measurable savings: baseline vs. optimized (in dollars)
• Deploy once, benefit across all teams using the same codebase

Internal Platform Teams & Shared Infrastructure

Challenge: Different teams query the same codebase; results are inconsistent.

NeuralMind Solution:

• Build the index once → share across all teams
• Cooccurrence learning adapts to your org's query patterns (neuralmind learn)
• Consistent, reproducible context for every question
• Single source of truth for "how does this system work?"

Teams Needing Offline/Disconnected Development

Challenge: Regulated environments, air-gapped networks, or unreliable connectivity.

NeuralMind Solution:

• No internet required after the initial install
• Pre-build the index on a connected machine, ship it in source control
• Works in submarines, rural offices, flight-mode development
• No API rate limiting or service outages

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🤔 Why NeuralMind vs. Heuristic-Only

Both approaches are valid; the tradeoff is retrieval quality vs. simplicity.

Approach	Token Reduction	Accuracy	Deps	Learns Over Time
Heuristic-only (no embeddings)	~33x (~97% fewer tokens)	70-80% top-5 (community baseline)	None	No
NeuralMind	40-70x	Project-dependent; evaluate against the same top-5 query set	ChromaDB	Yes (cooccurrence patterns)

NeuralMind does include a dependency (ChromaDB), but it still runs entirely offline — no API calls, no cloud services, no data leaves your machine.

If your priority is strict zero-dependency operation, heuristic-only is the simplest path. If your priority is stronger semantic retrieval and adaptive relevance, NeuralMind is the better fit.

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⚖️ NeuralMind vs. Alternatives

Short answers to "why not just use X?". Each row links to a deeper page.

Compared against	Short verdict
Cursor @codebase	Works only in Cursor; NeuralMind works in any agent and adds tool-output compression
Aider repo-map	Aider is syntactic only; NeuralMind adds semantic retrieval and compression
Sourcegraph Cody	Cody is server-hosted and org-wide; NeuralMind is local and per-project
Continue / Cline	Those are agent runtimes; NeuralMind is the context/compression layer underneath
GitHub Copilot	Copilot is hosted completions; NeuralMind is local context for any agent
Windsurf / Codeium	Vertically integrated IDE; NeuralMind is editor- and model-agnostic
Claude Projects	Projects reload all files every turn; NeuralMind retrieves only what the query needs
Prompt caching	Caching amortizes a big prompt; NeuralMind makes the prompt small — combine both
LangChain / LlamaIndex for code	Frameworks you assemble; NeuralMind is the assembled default for code agents
Long context windows (1M/2M)	Possible ≠ cheap — NeuralMind gives ~60× cost reduction on the same model
Generic RAG over a codebase	Text chunking loses structure; NeuralMind keeps the call graph
Tree-sitter / ctags / grep	Deterministic but syntactic; use alongside NeuralMind, not instead of

Full comparison index: docs/comparisons/.

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🚀 Quick Start (humans)

# Install
pip install neuralmind graphifyy

# Go to your project
cd your-project

# Generate knowledge graph (requires graphify)
graphify update .

# Build neural index
neuralmind build .

# (Optional) Install Claude Code PostToolUse compression hooks
neuralmind install-hooks .

# (Optional) Auto-rebuild on every git commit
neuralmind init-hook .

# Start using
neuralmind wakeup .
neuralmind query . "How does authentication work?"
neuralmind skeleton src/auth/handlers.py

---

🔧 How It Works

NeuralMind wraps a graphify knowledge graph (graphify-out/graph.json) in a ChromaDB vector store.
When you query it, a 4-layer progressive disclosure system loads only the context relevant to
your question.

┌─────────────────────────────────────────────────────────────┐
│ Layer 0: Project Identity (~100 tokens) — ALWAYS LOADED     │
│   Source: CLAUDE.md / mempalace.yaml / README first line    │
├─────────────────────────────────────────────────────────────┤
│ Layer 1: Architecture Summary (~500 tokens) — ALWAYS LOADED │
│   Source: Community distribution + GRAPH_REPORT.md          │
├─────────────────────────────────────────────────────────────┤
│ Layer 2: Relevant Modules (~300–500 tokens) — QUERY-AWARE   │
│   Source: Top 3 clusters semantically matching the query    │
├─────────────────────────────────────────────────────────────┤
│ Layer 3: Semantic Search (~300–500 tokens) — QUERY-AWARE    │
│   Source: ChromaDB similarity search over all graph nodes   │
└─────────────────────────────────────────────────────────────┘
Total: ~800–1,100 tokens vs 50,000+ for the full codebase

Prerequisites: NeuralMind requires graphify update . to have been run first. This produces:

• graphify-out/graph.json — the knowledge graph (required)
• graphify-out/GRAPH_REPORT.md — architecture summary (enriches L1, optional)
• graphify-out/neuralmind_db/ — ChromaDB vector store (created by neuralmind build)

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🖥️ Complete CLI Reference

neuralmind build

Build or incrementally update the neural index from graphify-out/graph.json.

neuralmind build [project_path] [--force]

Argument/Option	Default	Description
project_path	.	Project root containing graphify-out/graph.json
--force, -f	off	Re-embed every node even if unchanged

neuralmind build .
neuralmind build /path/to/project --force

Output: nodes processed, added, updated, skipped, communities indexed, build duration.

---

neuralmind wakeup

Get minimal project context for starting a session (~400–600 tokens, L0 + L1 only).

neuralmind wakeup <project_path> [--json]

neuralmind wakeup .
neuralmind wakeup . --json
neuralmind wakeup . > CONTEXT.md

---

neuralmind query

Query the codebase with natural language (~800–1,100 tokens, all 4 layers).

neuralmind query <project_path> "<question>" [--json]

neuralmind query . "How does authentication work?"
neuralmind query . "What are the main API endpoints?" --json
neuralmind query /path/to/project "Explain the database schema"

On first run from a TTY, you will be prompted once to enable local query memory logging.
Disable with NEURALMIND_MEMORY=0.

---

neuralmind search

Direct semantic search — returns code entities ranked by similarity to the query.

neuralmind search <project_path> "<query>" [--n N] [--json]

Option	Default	Description
--n	10	Maximum number of results
--json, -j	off	Machine-readable JSON output

neuralmind search . "authentication"
neuralmind search . "database connection" --n 5
neuralmind search . "PaymentController" --json

---

neuralmind skeleton

Print a compact graph-backed view of a file without loading full source (~88% cheaper than Read).

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

Option	Default	Description
--project-path	.	Project root (where the index lives)
--json, -j	off	Machine-readable JSON output

neuralmind skeleton src/auth/handlers.py
neuralmind skeleton src/auth/handlers.py --project-path /my/project
neuralmind skeleton src/auth/handlers.py --json

Output: function list with line numbers and rationales, internal call graph, cross-file edges
(imports, data sharing), and a pointer to the full source for when you need it.

---

neuralmind benchmark

Measure token reduction using a set of sample queries.

neuralmind benchmark <project_path> [--json]

neuralmind benchmark .
neuralmind benchmark . --json

---

neuralmind stats

Show index status and statistics.

neuralmind stats <project_path> [--json]

neuralmind stats .
neuralmind stats . --json   # {"built": true, "total_nodes": 241, "communities": 23, ...}

---

neuralmind learn

Analyze logged query history to discover module cooccurrence patterns. Improves future query
relevance automatically.

neuralmind learn <project_path>

neuralmind learn .

Reads .neuralmind/memory/query_events.jsonl, writes .neuralmind/learned_patterns.json.
The next neuralmind query applies boosted reranking automatically.

---

neuralmind install-hooks

Install or remove Claude Code PostToolUse compression hooks.

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

Option	Description
--global	Install in ~/.claude/settings.json (affects all projects)
--uninstall	Remove NeuralMind hooks only; preserves other tools' hooks

neuralmind install-hooks .                       # project-scoped
neuralmind install-hooks --global                # all projects
neuralmind install-hooks --uninstall             # remove project hooks
neuralmind install-hooks --uninstall --global    # remove global hooks

---

neuralmind init-hook

Install a Git post-commit hook that auto-rebuilds the index after every commit.
Safe and idempotent — coexists with other tools' hook contributions.

neuralmind init-hook [project_path]

neuralmind init-hook .
neuralmind init-hook /path/to/project

---

🔌 MCP Server

NeuralMind ships a Model Context Protocol server (neuralmind-mcp) that exposes all tools
to MCP-compatible agents.

Starting the server

neuralmind-mcp
# or
python -m neuralmind.mcp_server

Claude Desktop configuration

{
  "mcpServers": {
    "neuralmind": {
      "command": "neuralmind-mcp",
      "args": ["/absolute/path/to/project"]
    }
  }
}

Config file locations:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

Claude Code / Cursor project-scoped auto-registration

Drop a .mcp.json at your project root:

{
  "mcpServers": {
    "neuralmind": {
      "command": "neuralmind-mcp",
      "args": ["."]
    }
  }
}

MCP tool schemas

neuralmind_wakeup

{
  "project_path": "string (required) — absolute path to project root"
}

Returns:

{
  "context": "string",
  "tokens": 412,
  "reduction_ratio": 121.4,
  "layers": ["L0", "L1"]
}

neuralmind_query

{
  "project_path": "string (required)",
  "question":     "string (required) — natural language question"
}

Returns:

{
  "context": "string",
  "tokens": 847,
  "reduction_ratio": 59.0,
  "layers": ["L0", "L1", "L2", "L3"],
  "communities_loaded": [5, 12],
  "search_hits": 8
}

neuralmind_search

{
  "project_path": "string (required)",
  "query":        "string (required)",
  "n":            10
}

Returns array of:

{ "id": "node_id", "label": "authenticate_user", "file_type": "code",
  "source_file": "auth/handlers.py", "score": 0.92 }

neuralmind_skeleton

{
  "project_path": "string (required)",
  "file_path":    "string (required) — absolute or project-relative path"
}

Returns:

{ "file": "src/auth/handlers.py", "skeleton": "# src/auth/handlers.py ...", "chars": 620, "indexed": true }

neuralmind_build

{
  "project_path": "string (required)",
  "force":        false
}

Returns:

{
  "success": true,
  "nodes_total": 241,
  "nodes_added": 5,
  "nodes_updated": 2,
  "nodes_skipped": 234,
  "communities": 23,
  "duration_seconds": 3.1
}

neuralmind_stats

{ "project_path": "string (required)" }

Returns:

{ "built": true, "total_nodes": 241, "communities": 23, "db_path": "..." }

neuralmind_benchmark

{ "project_path": "string (required)" }

Returns:

{
  "project": "myapp",
  "wakeup_tokens": 341,
  "avg_query_tokens": 739,
  "avg_reduction_ratio": 65.6,
  "results": [...]
}

---

🪝 PostToolUse Compression

When neuralmind install-hooks has been run, Claude Code automatically applies these transforms
to every tool output before the agent sees it.

Read → skeleton

Raw source files are replaced with the graph skeleton (functions + rationales + call graph +
cross-file edges). This is ~88% smaller and contains the structural information agents need most.

To get the full source anyway:

NEURALMIND_BYPASS=1 <command>

Bash → filtered output

Long bash output is reduced to:

• All error/ERROR/FAIL/traceback/warning lines
• All summary lines (=====, passed, failed, Finished, Done in, etc.)
• Last 3 lines verbatim
• Header: [neuralmind: bash compressed, exit=N]

All errors and failures are always preserved. Routine pip/npm/build chatter is dropped.

Grep → capped results

Search results are capped at 25 matches with a [N more hidden] note appended.
Prevents context flooding from repository-wide searches.

Tunable thresholds

Variable	Default	Description
NEURALMIND_BYPASS	unset	Set to 1 to disable all compression
NEURALMIND_BASH_TAIL	3	Lines to keep verbatim from end of bash output
NEURALMIND_BASH_MAX_CHARS	3000	Below this size, bash output is not compressed
NEURALMIND_SEARCH_MAX	25	Max grep/search matches before capping
NEURALMIND_OFFLOAD_THRESHOLD	15000	Chars above which content is written to a temp file

---

🧠 Continual Learning

NeuralMind optionally learns from your query patterns to improve future relevance.

How it works

1. Collect — Each neuralmind query logs which modules appeared in the result to
   .neuralmind/memory/query_events.jsonl (opt-in, local only, zero overhead)
2. Learn — neuralmind learn . analyzes cooccurrence: which clusters appear together across queries
3. Improve — The next neuralmind query applies a +0.3 reranking boost to modules that
   co-occur with the current query's top matches
4. Repeat — The system gets smarter as you use it

Opt-in / consent

On first TTY query:

NeuralMind can keep local query memory (project + global JSONL) to improve future retrieval.
Enable? [y/N]:

Consent saved to ~/.neuralmind/memory_consent.json. Disable at any time:

export NEURALMIND_MEMORY=0     # disable query logging
export NEURALMIND_LEARNING=0   # disable pattern application

File locations

~/.neuralmind/
├── memory_consent.json             # consent flag
└── memory/
    └── query_events.jsonl          # global event log

<project>/.neuralmind/
├── memory/
│   └── query_events.jsonl          # project-specific events
└── learned_patterns.json           # created by: neuralmind learn .

Privacy

100% local — nothing is sent to any server. Delete ~/.neuralmind/ and <project>/.neuralmind/
at any time to remove all learning data.

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⏰ Keeping the Index Fresh

Automatic — Git post-commit hook (recommended)

neuralmind init-hook .

After every commit, the hook runs:

neuralmind build . 2>/dev/null && echo "[neuralmind] OK"

Manual

graphify update .
neuralmind build .

Scheduled — cron

0 6 * * * cd /path/to/project && graphify update . && neuralmind build .

CI/CD — GitHub Actions

- run: pip install neuralmind graphifyy
- run: graphify update . && neuralmind build .
- run: neuralmind wakeup . > AI_CONTEXT.md

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🔌 Compatibility

Component	Works With	Notes
CLI	Any environment	Pure Python, no daemon required
MCP Server	Claude Code, Claude Desktop, Cursor, Cline, Continue, any MCP client	pip install "neuralmind[mcp]"
PostToolUse Hooks	Claude Code only	Uses Claude Code's PostToolUse hook system
Git hook	Any git workflow	Appends to existing post-commit, idempotent
Copy-paste	ChatGPT, Gemini, any LLM	neuralmind wakeup . | pbcopy

Quick-start by tool

Claude Code — full two-phase optimization

pip install neuralmind graphifyy
cd your-project
graphify update .
neuralmind build .
neuralmind install-hooks .    # PostToolUse compression
neuralmind init-hook .        # auto-rebuild on commit (optional)

Then use MCP tools in sessions: neuralmind_wakeup, neuralmind_query, neuralmind_skeleton.

Cursor / Cline / Continue — MCP server

pip install "neuralmind[mcp]" graphifyy
graphify update .
neuralmind build .

Add to your MCP config:

{ "mcpServers": { "neuralmind": { "command": "neuralmind-mcp" } } }

ChatGPT / Gemini / any LLM — CLI + copy-paste

neuralmind wakeup . | pbcopy      # macOS — paste into chat
neuralmind query . "question"     # get context for a specific question

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✨ What's New in v0.3.x

Feature	Version	Details
Memory Collection	v0.3.0	Local JSONL storage for query events
Opt-in Consent	v0.3.0	One-time TTY prompt, env var overrides
EmbeddingBackend abstraction	v0.3.1	Pluggable vector backend (Pinecone/Weaviate ready)
Pattern Learning	v0.3.2	neuralmind learn . analyzes cooccurrence
Smart Reranking	v0.3.2	L3 results boosted by learned patterns
Accurate Build Stats	v0.3.3	Correctly distinguishes added vs updated nodes
Documentation polish	v0.3.4	CLI flags sync, Setup Guide, agent guidance in README

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📊 Benchmarks

NeuralMind benchmarks itself on every pull request. A hermetic fixture (tests/fixtures/sample_project/) plus a committed query set (tests/fixtures/benchmark_queries.json) runs through the full retrieval pipeline, and CI fails if aggregate reduction drops below a conservative floor (currently 4× on the small fixture — the fixture is intentionally tiny, real repos consistently hit 40–70× as shown below).

What CI measures on every PR

• Phase 1 — Reduction. Naive baseline (every .py file in the fixture concatenated) vs NeuralMind.query() output, per query. All tokens counted with tiktoken.
• Phase 2 — Learning uplift. Same queries run cold, then after seeding memory and running neuralmind learn. Reports the delta in reduction ratio and top-k retrieval hit rate. On a 500-line fixture the numerical uplift is modest by design — the test proves the mechanism persists, not that it's magic.
• Per-model breakdown. GPT-4o and GPT-4/3.5 counts are measured via real tiktoken encodings. Claude uses the Anthropic SDK tokenizer when available, else a clearly-labeled estimate derived from published vocab ratios. Llama is always estimated. No fabricated numbers anywhere.
• Memory persistence. tests/test_memory_persistence.py asserts events are logged, neuralmind learn produces a patterns file, and subsequent queries load it without error.

Community benchmarks

Real-world numbers submitted by users. Your code never leaves your machine — you submit a PR (or an issue, which a maintainer converts to a PR) with only the numbers. CI validates every entry against the schema and re-renders this table automatically.

Project	Lang	Nodes	Wakeup	Avg Query	Reduction	Model	Submitted
cmmc20	JavaScript	241	341	739	65.6×	Claude 3.5 Sonnet	@dfrostar · 2025-10-01
mempalace	Python	1,626	412	891	46.0×	Claude 3.5 Sonnet	@dfrostar · 2025-10-01

2 submission(s). See the JSON data for notes and verification commands.

Submit yours:

• Easy path: open a benchmark submission issue — fill out a form, a maintainer converts it to a PR.
• PR directly: add an entry to docs/community-benchmarks.json and run python scripts/render_community_table.py --inject README.md to regenerate the table. Schema: community-benchmarks.schema.json.

All entries include the exact neuralmind command that produced them, so reviewers (and any reader) can audit the numbers.

Reproduce locally (on our fixture)

pip install . tiktoken matplotlib graphifyy
graphify update tests/fixtures/sample_project
neuralmind build tests/fixtures/sample_project --force
python -m tests.benchmark.run          # phase 1 + phase 2
python -m tests.benchmark.multi_model  # per-model breakdown
python scripts/generate_chart.py       # refreshes the PNG above

Full machine-readable results land in tests/benchmark/results.json, human-readable report in tests/benchmark/report.md.

Reproduce on your code

Don't just trust numbers from our fixture — run it on your repo:

pip install neuralmind graphifyy
graphify update . && neuralmind build .
neuralmind benchmark . --contribute

Output shows your reduction ratio, tokens per query, and estimated monthly savings at Claude 3.5 Sonnet pricing. Full walkthrough: Does NeuralMind work on your codebase?

Retrieval quality baseline

• Heuristic-only baseline (community-reported): 70–80% top-5 retrieval accuracy
• NeuralMind target on the same query set: exceed that baseline via semantic retrieval + learned cooccurrence reranking

The pytest regression gate (tests/test_benchmark_regression.py) currently enforces ≥50% top-k hit rate on the fixture plus ≥4× reduction (low because the fixture is tiny; real repos measure 10× higher).

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❓ FAQ

How much does NeuralMind reduce Claude / GPT token costs?

Measured on real repos: 40–70× reduction per query (see Benchmarks). For a team running 100 queries/day on Claude Sonnet, that is roughly $450/month → $7/month. Exact savings depend on codebase size and model pricing.

Does NeuralMind work outside Claude Code?

Yes. The CLI works anywhere Python runs; the MCP server works with Cursor, Cline, Continue, Claude Desktop, and any MCP-compatible agent. For non-MCP tools like ChatGPT or Gemini, neuralmind wakeup . | pbcopy pipes context into a regular chat window. Only the PostToolUse compression hooks are Claude-Code-specific.

Does my code leave my machine?

No. NeuralMind is fully offline — no API calls, no cloud services. Embeddings run locally via ChromaDB, and the knowledge graph is stored in graphify-out/ in your project. Query memory (optional, opt-in) is written to .neuralmind/ on disk.

Is this RAG? How is it different from LangChain or LlamaIndex?

It is a form of RAG, but specialized for code. Instead of chunking text, NeuralMind retrieves over a knowledge graph of code entities (functions, classes, clusters) with a fixed 4-layer structure. That keeps the call graph intact and produces a token-budgeted output instead of a flat list of chunks. See vs. LangChain/LlamaIndex.

I have a 1M context window now — do I still need this?

Long context makes it possible to stuff a whole repo in; it does not make it cheap. You still pay per input token, so a 50K-token repo at Claude Sonnet rates costs ~$0.15 every turn. NeuralMind drops that to ~$0.002. See vs. long context.

Does it support my language?

Any language graphify supports (Python, JavaScript/TypeScript, and others via tree-sitter). NeuralMind consumes graphify-out/graph.json — if graphify can index it, NeuralMind can query it.

What is the difference between wakeup, query, and skeleton?

• wakeup — ~400 tokens of project orientation (L0 + L1). Run it at session start.
• query — ~800–1,100 tokens for a specific natural-language question (L0–L3).
• skeleton — compact view of a single file (functions + call graph + cross-file edges). Use before Read.

How does the PostToolUse compression work?

When neuralmind install-hooks . has been run, Claude Code invokes NeuralMind after every Read/Bash/Grep tool call but before the agent sees the output. Read becomes a skeleton (~88% smaller), Bash keeps errors + last 3 lines (~91% smaller), Grep caps at 25 matches. Set NEURALMIND_BYPASS=1 on any command to opt out.

Can I use NeuralMind without a knowledge graph?

No — the knowledge graph (graphify-out/graph.json) is the source of truth. Run graphify update . first, then neuralmind build ..

Does it auto-update when I change code?

Only if you install the git post-commit hook with neuralmind init-hook .. Otherwise run neuralmind build . manually; it is incremental and only re-embeds changed nodes.

What do I do if retrieval quality is poor on my repo?

1. Check that neuralmind stats . reports all your nodes indexed.
2. Run neuralmind benchmark . to see reduction ratios.
3. Enable query memory (it prompts on first TTY run) and periodically run neuralmind learn . — cooccurrence-based reranking improves relevance on your actual queries.
4. Open an issue with the query and expected result — retrieval quality is the thing we most want to improve.

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📚 Documentation

Resource	Contents
Setup Guide	First-time setup for Claude Code, Claude Desktop, Cursor, any LLM
CLI Reference	All commands and options
Learning Guide	Continual learning details
API Reference	Python API (NeuralMind, ContextResult, TokenBudget)
Architecture	4-layer progressive disclosure design
Integration Guide	MCP, CI/CD, VS Code, JetBrains
Troubleshooting	Common issues and fixes
Brain-like Learning	Design rationale for the learning system
Use Cases	Step-by-step walkthroughs: Claude Code, cost optimization, any-LLM, offline/regulated, growing monorepo
Comparisons	NeuralMind vs. Cursor, Copilot, Cody, Aider, Claude Projects, LangChain, long context, prompt caching, RAG, tree-sitter
USAGE.md	Extended usage examples

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🤝 Contributing

See CONTRIBUTING.md for guidelines.

📄 License

MIT License — see LICENSE for details.

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⭐ Star this repo if NeuralMind saves you money!