cortex-claude 0.6.0

Local-first, token-efficient memory system for Claude Code via MCP

Memory that remembers what matters. Built for Claude Code.

Quick Start • How It Works • Tools • Dashboard • Configuration • Benchmarks • Development

Cortex gives Claude Code persistent memory through a local MCP server. Unlike solutions that dump everything into context, Cortex uses progressive recall — a 3-layer retrieval system that returns only what's relevant, using the minimum tokens needed.

Interactive knowledge graph — explore entities, facts, and memories visually.

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The Problem

Memory solutions for AI assistants today waste tokens. They inject entire memory banks into every prompt, regardless of relevance. Cortex takes a different approach:

Save once:

"The auth service uses JWT tokens with 24-hour expiry. Refresh tokens are stored in httpOnly cookies."

Ask later, get back only what matters:

Layer 1: Facts (cheapest)
  auth service → use → jwt tokens
  auth service → use → hour expiry

Layer 2: Summary (~25% of original)

Layer 3: Full content (only if needed)

The system stops at the cheapest layer that answers the question. 66% fewer tokens on average.

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Key Features

• Progressive recall — 3 layers (facts → summaries → full content), stops at the cheapest sufficient layer
• Code graph — tree-sitter extracts symbols (functions, classes, calls, imports) from Python, JS, TS, Go, Java, Swift, Kotlin into the same knowledge graph. cortex_code(symbol) returns definition + callers + callees in ~100 tokens vs ~1000+ to read the file
• Auto-clustering — memories self-organize into semantic sub-graphs by embedding similarity. Labels derived from the most frequent entities. Navigate top-down via cortex_clusters
• Smart capture filter — heuristic gate (keywords, entity density, tool type) decides what to keep from auto-capture. Optional LLM-judge for ambiguous cases. No more polluting memory with ls and trivial reads.
• Knowledge graph — auto-extracts structured facts via spaCy NLP with multi-hop traversal
• Smart extraction — handles bullet lists, key:value pairs, comma lists, slash-separated tech, parentheticals, passive voice
• Claude fallback — optional Claude-assisted extraction when local NLP isn't enough
• Entity normalization — "postgres", "PostgreSQL", "pg" all resolve to the same entity
• Graph traversal — navigate entity connections across multiple hops (A → B → C)
• Hybrid search — vector similarity + FTS5 keyword search combined
• Configurable scopes — global, per-project, or custom memory boundaries
• Deduplication — detects and merges near-identical memories automatically
• Fact merging — when multiple memories mention the same fact, it's consolidated into one with boosted confidence
• Temporal awareness — facts detect when things happened ("in April 2024", "yesterday", "since v2") and attach timestamps
• Confidence recalibration — facts gain confidence when accessed frequently, lose it when contradicted by newer information
• Decay system — unused memories lose relevance over time, keeping results fresh
• Auto-capture — hooks automatically save tool results (Bash, Read, Grep, Edit, Write) to memory
• Session context injection — injects memory stats and known facts at session start
• Background daemon — pre-loaded model for instant saves via Unix socket (~0.3s vs ~5s cold start)
• Multi-language — EN, PT (auto-detected). ES, DE, FR with additional spaCy models
• Embedding model choice — 11 models supported, from fast (all-MiniLM, 384d) to high-quality (bge-large, 1024d). Auto-detects dimensions
• Local-first — SQLite + local embeddings + local NLP. Zero API calls, zero network, zero cost
• Privacy tags — wrap sensitive content in <private>...</private> to exclude it from memory
• Fully configurable — all thresholds, ratios, and behaviors via config.json

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Quick Start

One-Command Install

pip install cortex-claude && cortex-claude setup

That's it. The setup command:

• Configures the MCP server globally for Claude Code
• Installs auto-capture hooks (SessionStart + PostToolUse)
• Creates ~/.claude/CLAUDE.md with instructions for Claude to use Cortex automatically
• Downloads the embedding model (~80MB) and spaCy model (~12MB)
• Starts the background daemon for instant saves

Restart Claude Code and it works in every project, no per-project config needed. Claude will automatically consult Cortex before saying "I don't know" and save important context to memory.

With Claude-assisted extraction (optional)

pip install cortex-claude[claude]

Manual Setup (alternative)

If you prefer manual configuration, add a .mcp.json to your project root:

{
  "mcpServers": {
    "cortex": {
      "type": "stdio",
      "command": "python3",
      "args": ["-m", "cortex_claude"]
    }
  }
}

Use

Just talk to Claude naturally. Cortex works in the background:

"Remember that the API uses rate limiting at 500 req/min"
"What do you know about rate limiting?"
"What facts do you have about the API?"
"What's connected to the auth service?"
"Forget what I said about the old API key"
"Show me the memory status"

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Tools

Cortex exposes 10 MCP tools to Claude Code:

Tool	What it does	Token cost
cortex_save	Store memory with auto fact extraction, summarization, and embedding	N/A
cortex_recall	Progressive retrieval: facts → summaries → full content	Controlled via max_tokens
cortex_facts	Direct knowledge graph query, returns structured triplets	~5-15 tokens per fact
cortex_traverse	Navigate the knowledge graph; accepts start="cluster:42" to begin from a sub-graph	~5-15 tokens per connection
cortex_code	Look up a code symbol: definition, callers, callees, mentions	~50-150 tokens vs ~1000+ to read the file
cortex_index_code	Index a file or directory into the code graph (Python, JS/TS, Go, Java, Swift, Kotlin)	N/A
cortex_clusters	List or rebuild memory sub-graphs (auto-formed by similarity)	~10 tokens per cluster
cortex_forget	Delete memories by query or ID (dry-run by default)	N/A
cortex_scopes	Manage scopes: list, create, delete, link/unlink directories	N/A
cortex_status	Dashboard: memory count, fact count, storage size per scope	N/A

Recall Depth Modes

Mode	Returns	When to use
auto	Starts cheap, escalates if needed	Default — best for most queries
facts	Only knowledge graph triplets	Quick lookups, minimal token use
summaries	Facts + compressed summaries	Medium detail needed
full	All layers including original text	Full context needed

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How It Works

Save: content → embedding + fact extraction + summarization → SQLite

Recall (progressive):
  1. Facts layer     (~5-15 tokens/fact)   → sufficient? stop
  2. Summaries layer (~25% of original)    → sufficient? stop
  3. Full chunks     (original content)    → return

Fact Extraction

Three methods combined for maximum coverage:

1. spaCy NLP — dependency parsing, NER, passive voice handling, conjunction expansion
2. Pattern matching — bullet lists (- X for Y), key:value, comma lists, slash-separated (React/TypeScript), parentheticals (FastAPI (Python)), with/for constructs
3. Claude fallback (opt-in) — when local extraction produces < 2 high-confidence facts, falls back to Claude Haiku. Off by default.

Entities are normalized and deduplicated: "postgres" → "postgresql", "js" → "javascript", "k8s" → "kubernetes".

Graph Traversal

Navigate entity connections across multiple hops:

auth → JWT → express-jwt → middleware
  ↓
  httpOnly cookies

Query cortex_traverse("auth") and discover everything connected.

Decay

Memories that aren't accessed lose relevance over time:

score = e^(-lambda * days) * (1 + log(access_count))

Recalculated on server startup. Frequently accessed memories get boosted. Stale ones fade.

Auto-Capture & Hooks

Cortex uses Claude Code hooks to work automatically:

• SessionStart — injects memory stats and known facts when you open a session. Claude knows it has memory and consults it before saying "I don't know".
• PostToolUse — captures results from all tools in background: Bash, Read, Edit, Write, Grep, Glob, Agent, WebSearch, WebFetch, and all third-party MCP tools. Code files (Python, JS/TS, Go, Java, Swift, Kotlin) trigger an additional index_code step that extracts symbols into the code graph.
• Capture filter — before persisting, every auto-captured save passes through a heuristic gate (size, signal keywords, tool type, entity density). ls, trivial reads, and noisy edits are dropped. Ambiguous cases can optionally consult an LLM judge.
• Background Daemon — keeps the embedding model pre-loaded via Unix socket. First save after boot: ~5s (model load). Subsequent saves: ~0.3s. On the first startup after upgrading to v0.6.0 (schema v7), the daemon auto-backfills clusters for any scope with memories but no clusters yet.

All hooks are installed globally by cortex-claude setup. No per-project config needed.

Code Graph

Tree-sitter parses your source files into structured facts in the same knowledge graph used for memories:

my_func   → defined_in  → /path/to/file.py:42
my_func   → in_language → python
my_func   → calls       → other_func
MyClass   → extends     → BaseClass
sample    → imports     → json

Trigger manually with cortex_index_code(path) for a directory, or let auto-capture index files as you read/edit them. Look up symbols with cortex_code(symbol) — returns definition, callers, callees, extends, imports, and which memories mention it. Supported languages: Python, JavaScript, TypeScript/TSX, Go, Java, Swift, Kotlin.

When a saved memory mentions a known symbol, Cortex automatically creates a memory:<id> → mentions → <symbol> fact, linking decisions and bug reports to the code they reference.

Memory Clusters (Sub-graphs)

As memories accumulate, Cortex groups them into semantic clusters using cosine similarity on their embeddings. Each cluster gets a human-readable label derived from the most frequent entities in its facts (e.g. "embeddings, vectors, sqlite-vec").

# List clusters
cortex_clusters

# Traverse the graph starting from a cluster
cortex_traverse start="cluster:42"

# Rebuild clusters after tuning similarity_threshold
cortex_clusters action="backfill"

Clustering runs incrementally in the background after every N saves (default 20, with a 5-minute cooldown). The default similarity_threshold=0.70 balances cluster coherence with singleton noise — tune it in config.json if your corpus needs tighter or looser grouping.

Privacy

Wrap sensitive content in <private> tags to exclude it from memory:

The API uses JWT for auth. <private>API_KEY=sk-abc123secret</private> Tokens expire in 24h.

Cortex strips everything between <private>...</private> before saving. Works in both manual saves and auto-capture. If the entire content is private, nothing is saved.

Hybrid Search

Combines vector similarity (semantic meaning) with FTS5 (exact keyword match) for best recall. FTS5 synced automatically via SQLite triggers.

Web Dashboard

Interactive knowledge graph visualization and memory browser:

cortex-claude web
# Opens at http://localhost:37800

Features:

• Interactive knowledge graph — nodes are entities, edges are relations. Click a node to see all its facts and related memories.
• Memory browser — browse all memories with search, tags, scope, and decay score.
• Facts list — all extracted triplets, click to focus on the graph node.
• Live stats — memory count, fact count, scopes, storage size.
• Dark theme — designed for developers.

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Cortex vs Traditional Memory (claude-mem, etc.)

Most memory solutions for AI assistants follow the same pattern: capture observations, compress them, inject into every prompt. Cortex takes a fundamentally different approach.

	Traditional (claude-mem)	Cortex
Storage model	Compressed text / summaries	Knowledge graph (structured triplets) + summaries + full text
Retrieval	Auto-inject into every session (~500-2000 tokens)	Progressive recall: facts → summaries → full (~50-100 tokens)
Intelligence	Linear summaries	Structured facts with entity relationships + graph traversal
Search	Keyword / vector	Hybrid: semantic embedding + FTS5 keyword + graph traversal
Extraction	Captures tool call observations	NLP fact extraction (spaCy + patterns + optional Claude)
Entity awareness	None	"postgres" = "postgresql" = "pg" (normalized + fuzzy match)
Graph navigation	None	Multi-hop traversal (A → B → C)
Staleness	No decay	Unused memories lose relevance over time
Duplicates	Can accumulate	Auto-merged (cosine similarity > 0.92)
Auto-capture	All tool calls via hooks	All tools (Bash, Read, Edit, Write, Grep, Glob, Agent, MCP, Web) via hooks + daemon
Session injection	Full context dump on start	Lightweight facts injection via direct SQLite (<1s)
Dependencies	Node.js, Bun, Chroma vector DB	Python + SQLite only (zero external services)
Web UI	Viewer on localhost:37777	Interactive graph dashboard on localhost:37800

Where Cortex wins

• Token efficiency — 66% fewer tokens returned. Progressive recall stops at the cheapest sufficient layer.
• Structured understanding — knowledge graph with traversal vs flat text. Ask "what's connected to auth?" and get real graph navigation.
• Entity intelligence — normalizes and deduplicates entities across memories. "postgres", "PostgreSQL", and "pg" are the same thing.
• Freshness — decay system ensures frequently accessed memories rank higher. Old, unused memories fade.
• Zero external services — no Chroma, no Bun, no Node.js. Just Python + SQLite.
• Multi-language — fact extraction works in EN, PT (auto-detected), with ES/DE/FR support.

Where claude-mem wins

• Broader auto-capture — captures all tool calls including MCP tools from third-party servers.
• Web viewer — real-time memory browser (Cortex has an interactive graph dashboard, but claude-mem's is more mature).
• One-command install — npx claude-mem install vs manual MCP config.
• Larger community — more stars, Discord, extensive documentation site.

The fundamental difference

Traditional memory asks "what happened?" — Cortex asks "what matters?"

Traditional solutions observe and replay. Cortex understands, structures, and retrieves surgically. The result: fewer tokens, more relevant answers, and a knowledge graph that grows smarter over time.

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Benchmarks

With 10 stored memories (244 total tokens):

Depth	Tokens returned	Reduction	Latency
facts	82	66%	~10ms
auto	82	66%	~10ms
full	244	0%	~12ms

Operation	Latency
cortex_facts query	0.1ms
Graph traversal (2 hops)	0.2ms
Save (after model load)	~30ms

Run benchmarks yourself:

uv run python scripts/benchmark.py

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Configuration

All behavior is customizable via ~/.cortex-claude/config.json:

{
  "recall": {
    "default_max_tokens": 200,
    "default_depth": "auto",
    "sufficiency": {
      "coverage_threshold": 0.7,
      "confidence_threshold": 0.6
    }
  },
  "embeddings": {
    "model": "all-MiniLM-L6-v2",
    "batch_size": 32,
    "_available_models": [
      "all-MiniLM-L6-v2 (384d, 80MB, fast)",
      "all-mpnet-base-v2 (768d, 420MB, medium)",
      "BAAI/bge-small-en-v1.5 (384d, 130MB, fast)",
      "BAAI/bge-base-en-v1.5 (768d, 440MB, medium)",
      "BAAI/bge-large-en-v1.5 (1024d, 1.3GB, best quality)",
      "intfloat/e5-large-v2 (1024d, 1.3GB, best quality)",
      "intfloat/multilingual-e5-small (384d, 470MB, multilingual)"
    ]
  },
  "facts": {
    "extraction_method": "local",
    "min_confidence": 0.5,
    "claude_fallback": false,
    "claude_confidence_threshold": 0.5
  },
  "decay": {
    "lambda": 0.05,
    "recalculate_interval_hours": 6,
    "min_score": 0.01
  },
  "deduplication": {
    "similarity_threshold": 0.92,
    "merge_strategy": "append"
  },
  "scopes": {
    "mappings": {
      "/path/to/project-a": "project:a",
      "/path/to/project-b": "project:b"
    },
    "default": "global",
    "search_order": "project_first"
  },
  "storage": {
    "max_db_size_mb": 500
  }
}

All fields are optional. Defaults are used for anything not specified.

See examples/ for ready-to-use configuration files.

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Development

git clone https://github.com/rafaelaugustos/cortex-claude.git
cd cortex-claude
uv venv --python python3.13
uv sync --all-extras
uv run python -m spacy download en_core_web_sm
uv run pytest

# Run the demo
uv run python scripts/demo.py

# Run benchmarks
uv run python scripts/benchmark.py

See CONTRIBUTING.md for contribution guidelines.

Architecture

See ARCHITECTURE.md for the full technical specification.

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Something Missing?

We'd love to hear from you. Open an issue on GitHub:

Found a bug?

1. Go to Issues
2. Describe what happened vs. what you expected
3. Include your Python version, OS, and steps to reproduce

Have a feature request?

1. Go to Issues
2. Describe the problem you're trying to solve
3. Suggest a solution if you have one

Want to contribute?

1. Check CONTRIBUTING.md for guidelines
2. Look for issues labeled good first issue
3. Fork, branch, code, test, PR

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License

MIT — see LICENSE.

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Built with Python • Powered by Claude Code • Made by Rafael Augusto