neurodex 0.3.0

Complete project memory for AI code assistants. One call, full context, zero guessing.

NEURODEX

Complete project memory for AI code assistants. One call, full context, zero guessing.

NEURODEX gives LLMs persistent, symbol-level knowledge of your entire codebase across sessions. No extra AI models, no cloud, no API keys. Built on SQLite FTS5 and tree-sitter.

pip install neurodex
neurodex init                 # index your project
neurodex install              # wire into Claude Code / Codex

What It Does

Your AI assistant starts every session knowing nothing. NEURODEX fixes that.

Without NEURODEX                          With NEURODEX
─────────────────────                   ─────────────────────
Session starts → blank                  Session starts → neurodex_brain()
"What is this project?" → read 10+     → 14k tokens: every module,
  files, still incomplete                 every function signature,
"Fix the auth bug" → grep, read 5        every dependency, every
  more files, guess at structure          past decision
Total: 20+ file reads                  Total: 0 file reads to start

Architecture

graph TB
    subgraph "Index Time (pure algorithmic, no AI)"
        TS[tree-sitter AST] --> CH[Chunker]
        CH --> FTS[SQLite FTS5]
        CH --> NODES[Symbol Nodes]
        CH --> EDGES[Typed Edges]
    end

    subgraph "Query Time"
        BRAIN[Brain Generator] --> |reads| FTS
        BRAIN --> |reads| NODES
        BRAIN --> |reads| EDGES
        SEARCH[BM25 Search] --> |queries| FTS
        IMPACT[Impact Analysis] --> |traverses| EDGES
        REFS[Reference Finder] --> |scans| FTS
        REFS --> |scans| EDGES
        XPROJ[Cross-Project] --> |bridges| EDGES
    end

    subgraph "MCP Server"
        LLM[Claude / Codex] --> |neurodex_brain| BRAIN
        LLM --> |neurodex_search| SEARCH
        LLM --> |neurodex_impact| IMPACT
        LLM --> |neurodex_references| REFS
        LLM --> |neurodex_cross_impact| XPROJ
        LLM --> |neurodex_save| FTS
    end

How It Works

Session Start

sequenceDiagram
    participant LLM as Claude / Codex
    participant MCP as NEURODEX MCP Server
    participant DB as SQLite (local)

    LLM->>MCP: neurodex_brain()
    MCP->>DB: Read nodes, edges, chunks, insights
    MCP-->>LLM: Complete project brain (~14k tokens)
    Note over LLM: Now knows every module,<br/>function signature, dependency,<br/>and past session decision
    LLM->>LLM: Ready to work (zero file reads)

Making a Change

sequenceDiagram
    participant User
    participant LLM as Claude / Codex
    participant MCP as NEURODEX MCP Server

    User->>LLM: "Rename BrandProfile to BrandIdentity"
    LLM->>MCP: neurodex_references("BrandProfile")
    MCP-->>LLM: 13 references in 13 files with exact lines
    LLM->>MCP: neurodex_impact("brands/models.py")
    MCP-->>LLM: 20 affected symbols, risk 0.73
    LLM->>MCP: neurodex_cross_impact("brands/models.py")
    MCP-->>LLM: 3 cross-project contracts affected
    LLM->>LLM: Makes targeted edits (reads only lines it changes)
    LLM->>MCP: neurodex_save("Renamed BrandProfile → BrandIdentity")
    Note over MCP: Saved for future sessions

Cross-Project Awareness

graph LR
    subgraph Backend
        BE_ROUTE[POST /auth/login] --> BE_SVC[AuthService.login]
        BE_SVC --> BE_REPO[UserRepository]
    end

    subgraph Frontend
        FE_PAGE[LoginPage.tsx] --> FE_API[fetch '/auth/login']
    end

    subgraph Mobile
        MOB_SCREEN[LoginScreen.dart] --> MOB_API[api.post '/auth/login']
    end

    BE_ROUTE -.->|contract| FE_API
    BE_ROUTE -.->|contract| MOB_API

    style BE_ROUTE fill:#f96
    style FE_API fill:#f96
    style MOB_API fill:#f96

When you change a backend endpoint, neurodex_cross_impact finds every frontend and mobile file that consumes it.

MCP Tools

Tool	Purpose
neurodex_brain	Complete project brain. Call first on session start.
neurodex_search	BM25 full-text search with synonym expansion
neurodex_compact_search	Metadata-only search (saves tokens)
neurodex_symbols	Find functions/classes by name pattern
neurodex_save	Persist a decision or insight for future sessions
neurodex_references	Find ALL references to a symbol across the project
neurodex_impact	Blast-radius: what breaks if you change this file?
neurodex_cross_impact	Cross-project: what breaks in other repos?
neurodex_trace	Follow import/dependency chains
neurodex_brain	Complete project context in one call
neurodex_status	Index health and project info
neurodex_list_projects	All indexed repos and workspaces
neurodex_workspace_create	Group repos for cross-repo search
neurodex_set_context	Set session search scope

Project Brain

The brain is not a markdown file. It is a compressed, structured representation of the entire project that the LLM processes in full.

PROJECT: ContentPlatform
  AI-powered SaaS for brand social content generation
  Stack: FastAPI, PostgreSQL, SuperTokens, Celery+Redis

MODULES:
  [auth] User authentication, JWT, Google/Apple OAuth
    files: models.py, oauth.py, repository.py, router.py, security.py, service.py
    · service.py:27-77 class AuthService
    · service.py:49-77 async def login(email: str, password: str) → LoginResponse
    · security.py:15-28 def create_access_token(user_id: str) → str
    § User: email(str), password_hash(str | None), full_name(str)
    § LoginResponse: access_token(str), refresh_token(str), expires_in(int)
    uses: common, core, organizations

  [brands] Brand profiles, RAG persona builder
    · models.py:29-84 class BrandProfile(BaseModel, TenantMixin)
    · persona_builder.py:23-25 build_brand_persona_from_url(url: str)
    § BrandProfile: name(String), voice_summary(Optional[str]), colors(Optional[dict])
    uses: common, core, generation

KEY FLOWS:
  [API] POST /auth/login (auth) → common → core
  [API] POST /brands/{id}/analyze (brands) → common → generation
  [TASK] execute_generation_job (tasks) → core

MEMORY:
  ! Brand colors extracted via Playwright screenshot, NOT HTML parsing
  ! N+1 in analytics fixed with selectinload, don't remove it

Every symbol has its file and exact line range. The LLM can target service.py:49-77 without reading the file first.

Setup

Install

pip install neurodex

Index a Project

cd your-project
neurodex init

Wire into Claude Code

neurodex install

This adds the MCP server to ~/.claude/settings.json and injects usage instructions into your project's CLAUDE.md.

Index Multiple Projects

cd backend && neurodex init
cd ../frontend && neurodex init
cd ../mobile && neurodex init

Create a Workspace (Cross-Repo Search)

neurodex workspace create "MyApp" /path/to/backend /path/to/frontend /path/to/mobile

CLI Commands

Command	Description
neurodex init [path]	Index a project directory
neurodex status	Show all indexed projects and health
neurodex brain [path]	Generate and display the project brain
neurodex search "query"	Test search from terminal
neurodex reindex [path]	Force full re-index
neurodex workspace create NAME [paths...]	Create a workspace
neurodex workspace add NAME path	Add repo to workspace
neurodex workspace list	List all workspaces
neurodex auto-save	Extract insights from Claude Code history
neurodex install	Add MCP server to Claude Code settings

Benchmarks

Tested against ContentPlatform (342 files, 314 indexed):

Metric	Score
Hit@1 (correct file is top result)	75%
Recall@3 (correct file in top 3)	90%
Recall@5 (correct file in top 5)	95%
MRR (mean reciprocal rank)	0.838
Brain tokens (full project)	~14k
Index time	0.7s

Cross-project on GakkoDeck (4 repos, 1542 files):

Metric	Score
Brain tokens (all 4 projects)	~14k
Context window usage	6.9% of 200k
Cross-project contract detection	16 contracts matched

What Gets Indexed

Data	Storage	Method
Code symbols	Nodes table	tree-sitter AST (18 languages)
Full-text content	Chunks + FTS5	BM25 inverted index
Import relationships	Edges table	Regex + AST
Call relationships	Edges table	Regex heuristic
Inheritance chains	Edges table	AST class parsing
Test coverage links	Edges table	File + function pattern matching
Session insights	Chunks table	Explicit neurodex_save calls
API endpoints	Extracted at query time	Route decorator parsing
Cross-project contracts	Computed at query time	Endpoint-to-consumer matching

Language Support

18 languages with AST parsing: Python, JavaScript, TypeScript, Go, Rust, Java, C, C++, C#, Ruby, PHP, Swift, Kotlin, Scala, Dart, Elixir, Haskell, Lua

16 languages with regex fallback: SQL, Bash, Markdown, YAML, TOML, JSON, XML, HTML, CSS, SCSS, Vue, Svelte, Jupyter, and more

Tech Stack

Component	Choice
Storage + Search	SQLite FTS5 (built into Python)
AST Parsing	tree-sitter
File Watching	watchdog
MCP Framework	mcp (official Python SDK)
CLI	click
Extra AI Models	None

Zero external services. Everything runs locally. Total install size ~20MB.

License

MIT