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Cognitive engine for AI agents — semantic memory, observations, embeddings, dream consolidation. Cloud Run service + MCP tools.

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# @fozikio/cortex-engine

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Persistent memory for AI agents. Open source, LLM-agnostic, works with any MCP client.

## Star History

## What It Does

Most AI agents forget everything when the session ends. `cortex-engine` fixes that — it gives agents a persistent memory layer that survives across sessions, models, and runtimes.

- **Semantic memory** — store and retrieve observations, beliefs, questions, and hypotheses as interconnected nodes
- **Belief tracking** — agents hold positions that update when new evidence contradicts them
- **Two-phase dream consolidation** — NREM compression (cluster, refine, create) + REM integration (connect, score, abstract) — modeled on biological sleep stages
- **Goal-directed cognition** — `goal_set` creates desired future states that generate forward prediction error, biasing consolidation and exploration toward what matters
- **Neuroscience-grounded retrieval** — GNN neighborhood aggregation, query-conditioned spreading activation, multi-anchor Thousand Brains voting, epistemic foraging
- **Information geometry** — locally-adaptive clustering thresholds that respect embedding space curvature, schema congruence scoring
- **Graph health metrics** — Fiedler value (algebraic connectivity) measures knowledge integration; PE saturation detection prevents identity model ossification
- **Spaced repetition (FSRS)** — interval-aware scheduling with consolidation-state-dependent decay profiles
- **Embeddings** — pluggable providers (built-in, OpenAI, Vertex AI, Ollama) — no external service required by default
- **LLM-agnostic** — pluggable LLM providers: Ollama (free/local), Gemini, Kimi (Moonshot AI), DeepSeek, Hugging Face, OpenRouter, OpenAI, or any OpenAI-compatible API
- **Three storage backends** — local SQLite (default), cloud Firestore, and JSON file (backup/migration). All share one `CortexStore` interface — see [docs/storage-backends.md](docs/storage-backends.md)
- **Atomic transactions** — `withTransaction(fn)` primitive composes multi-step writes. SQLite uses `BEGIN IMMEDIATE` with a per-store mutex; Firestore uses `runTransaction` with a write-routing proxy. See [docs/concurrency.md](docs/concurrency.md)
- **Migration tooling** — `fozikio migrate --from <url> --to <url>` clones between any pair of backends. ID-preserving, checkpointed, resumable, fails-loud on schema mismatch
- **Typed tool catalogue** — every cognitive tool carries `category` + `whenToUse` + `doNotUse` metadata so LLMs disambiguate cleanly. Browse with `fozikio tools` or `GET /tools`. Auto-generated reference at [docs/tools-reference.md](docs/tools-reference.md)
- **Long-context dream consolidation** — set `strategy: long-context` to run edge discovery and abstraction in a single large LLM pass instead of N² pairwise calls; surfaces transitive patterns and cross-domain connections that the sequential approach misses
- **Agent dispatch** — `agent_invoke` lets your agent spawn cheap, cortex-aware sub-tasks using any configured LLM. Knowledge compounds across sessions.
- **MCP server** — 60 cognitive tools (`query`, `observe`, `believe`, `wander`, `dream`, `goal_set`, `agent_invoke`, `thread_create`, `journal_write`, `evolve`, etc.) over the Model Context Protocol

The result: personality and expertise emerge from accumulated experience, not system prompts. An agent with 200 observations about distributed systems doesn't need to be told "you care about distributed systems." It just knows.

Works with Claude Code, Cursor, Windsurf, or any MCP-compatible client. Runs locally (SQLite) or in the cloud (Firestore + Cloud Run).

## Security

The engine includes defense-in-depth protections for deployed environments:

- **Timing-safe auth** — REST server authentication uses `crypto.timingSafeEqual` to prevent timing side-channel attacks
- **Plugin sandboxing** — the plugin loader validates import paths against trusted directories, blocking loads from untrusted locations
- **REST tool blocklist** — destructive tools (`forget`, `dream`, `evolve`, `resolve`, `thread_resolve`) are blocked from the generic REST endpoint; they remain available via MCP for direct agent access
- **SQLite injection prevention** — namespace names are validated (alphanumeric only), LIMIT clauses are parameterized
- **Secret leak prevention** — config loader warns when API keys appear in config files instead of environment variables

### Known advisories

`npm install @fozikio/cortex-engine` currently reports **3 moderate advisories**. All three are the same upstream issue counted at three levels of one dependency chain, and none are reachable in this package:

```
@fozikio/cortex-engine
└── @modelcontextprotocol/sdk@1.29.0   (latest)
    └── @hono/node-server ^1.19.9      ← GHSA-frvp-7c67-39w9
```

**What it is:** path traversal in `@hono/node-server`'s `serve-static` middleware on Windows, via an encoded backslash (`%5C`).

**Why it isn't fixed:** the advisory's first patched version is `2.0.5` — a major-version bump the MCP SDK has not taken. `@modelcontextprotocol/sdk@1.29.0` is the current latest and still pins `^1.19.9`, so there is no remediation available downstream. Forcing `2.x` via an override would break the SDK's expected API.

**Why it doesn't affect you:** cortex-engine never imports hono. `@hono/node-server` is pulled in only as a transitive dependency of the MCP SDK, and the MCP server here runs over **stdio transport**, which never mounts `serve-static`. The dashboard's static file serving is our own implementation ([`src/rest/server.ts`](src/rest/server.ts)), which resolves paths and verifies containment with `path.relative` before reading — explicitly handling the Windows backslash case this advisory describes.

This will clear on its own once the MCP SDK adopts `@hono/node-server` 2.x. Until then, `npm audit` noise from this chain is expected and safe to ignore.

## Architecture

| Module | Role |
|--------|------|
| `core` | Foundational types, config, and shared utilities |
| `engines` | Cognitive processing: memory consolidation, FSRS, graph traversal |
| `stores` | Persistence layer — SQLite (local), Firestore (cloud), JSON (backup/migration). All implement the shared `CortexStore` interface |
| `tools` | All 60 cognitive tool implementations (one file per tool) |
| `mcp` | MCP server, tool registry, and plugin loader |
| `cognitive` | Higher-order cognitive operations (dream, wander, validate) |
| `triggers` | Scheduled and event-driven triggers |
| `bridges` | Adapters for external services and APIs |
| `providers` | Embedding and LLM provider implementations |
| `bin` | Entry points: `serve.js` (HTTP + MCP), `cli.js` (admin CLI) |
| `public` | Built-in web dashboard (served automatically with `--rest`) |

## Quick Start

```bash
npm install @fozikio/cortex-engine
npx fozikio init my-agent
cd my-agent
npx fozikio serve   # starts MCP server
```

Your agent now has 60 cognitive tools. The generated `.mcp.json` is version-pinned and platform-aware (Windows `cmd /c` wrapper handled automatically).

See the **[Quick Start](docs/quick-start.md)** guide for the full 5-minute setup.

### Multi-Agent

```bash
npx fozikio agent add researcher --description "Research agent"
npx fozikio agent add trader --description "Trading signals"
npx fozikio agent generate-mcp   # writes .mcp.json with scoped servers
```

Each agent gets isolated memory via namespaces. See the **[Architecture](#architecture)** section for details.

### Agent-First Setup

The fastest path: open an AI agent in an empty directory and say *"set up a cortex workspace."* The agent runs `npx fozikio init`, reads the generated files, and is immediately productive. See the **[Agent-First Setup](docs/agent-first-setup.md)** guide for the full walkthrough.

### Dashboard

cortex-engine ships with a built-in web dashboard. Start the REST server and open the URL in your browser:

```bash
npx fozikio serve --rest --port 3000
# open http://localhost:3000
```

The dashboard shows your agent's stats, threads, ops log, memories, concepts, and observations — no separate install required. It auto-detects its API from the same origin it's served from.

If auth is enabled (`CORTEX_API_TOKEN`), the dashboard loads without auth but API calls require a token. Set it via localStorage:

```js
localStorage.setItem("cortex-settings", JSON.stringify({ token: "your-token" }));
```

Source: [fozikio-dashboard](https://github.com/Fozikio/Dashboard)

### CLI

Run `fozikio` with no arguments for an interactive session — a prompt with tab
completion, history, and a filterable command palette on an empty enter:

```
  fozikio 1.3.0
  ● ollama  ● nli

enter a command · empty enter to browse · ? help · exit quit

fozikio ›
```

Or use it directly:

```bash
npx fozikio doctor                         # diagnose the install, with fixes
npx fozikio dashboard                      # live service and memory view
npx fozikio up                             # start every service, wait until ready
npx fozikio status                         # service status (exit 1 if unhealthy)
npx fozikio down                           # stop every service
npx fozikio serve                          # start MCP server
```

**Services.** The default setup (`--embed ollama --llm ollama`, plus NLI adjudication)
depends on two background daemons: ollama on `:11434` and the NLI cross-encoder on
`:11435`. When either stops answering, every semantic tool — `query`, `observe`,
`wonder`, `dream` — fails while ops, threads and journal keep working, so the failure
is easy to miss. `fozikio` supervises both:

```bash
npx fozikio service start nli              # start detached, wait for the probe
npx fozikio service status                 # per-service state
npx fozikio service logs ollama --lines 50 # tail ~/.fozikio/logs/
npx fozikio service restart ollama
npx fozikio up --watch                     # restart on failure, with backoff
```

A service counts as up when its HTTP endpoint answers, not when its process exists —
a process that is alive but no longer responding reports as `degraded`, which is the
failure this is built to catch.

**Memory.**

```bash
npx fozikio memory health                  # memory health report
npx fozikio memory vitals                  # behavioral vitals and prediction error
npx fozikio memory wander --from "auth"    # seeded walk through the graph
npx fozikio memory maintain fix            # scan and repair data issues
npx fozikio memory report                  # weekly quality report
npx fozikio tools --category memory        # browse the cognitive tool catalogue
npx fozikio migrate --from sqlite:./cortex.db --to json:./backup.json --verify
```

The pre-`memory` spellings (`fozikio health`, `fozikio vitals`, …) still work and are
not deprecated — existing scripts need no changes.

Every command takes `--json` for machine-readable output and honours `NO_COLOR`;
styling and progress indicators switch off automatically when output is piped.
`--yes` skips confirmations for unattended use. Read-only commands honour
`--namespace <ns>` and `--agent <name>`; in a workspace with `.fozikio/agent.yaml`,
the agent's `default_namespace` is picked up automatically — no flag needed.

### Development

```bash
npm run dev       # tsc --watch
npm test          # vitest run
npm run test:watch
```

## Environment Variables

| Variable | Required | Description |
|----------|----------|-------------|
| `CORTEX_API_TOKEN` | Optional | Used by the `cortex-telemetry` hook to send retrieval feedback to the cortex API. Not required to run the MCP server. |
| `MOONSHOT_API_KEY` | Optional | Required when `llm: kimi` is set. Get one from [platform.moonshot.cn](https://platform.moonshot.cn). |
| `OPENAI_API_KEY` | Optional | Required when `llm: openai` is set, or when using any OpenAI-compatible provider without an explicit API key. |

Additional variables are required depending on which providers you enable (Firestore, Vertex AI, etc.). See `docs/` for provider-specific configuration.

## Rules, Skills & Agents

`fozikio init` automatically installs safety rules, skills, and agent definitions from the `fozikio.json` manifest into the target workspace.

### Safety Rules (Reflex)

cortex-engine ships with [Reflex](https://github.com/Fozikio/reflex) rules — portable YAML-based guardrails that work across any agent runtime, not just Claude Code.

| Rule | Event | What It Does |
|------|-------|-------------|
| `cognitive-grounding` | `prompt_submit` | Nudges the agent to call `query()` before evaluation, design, review, or creation work |
| `observe-first` | `file_write` / `file_edit` | Warns if writing to memory directories without calling `observe()` or `query()` first |
| `note-about-doing` | `prompt_submit` | Suggests capturing new threads of thought with `thread_create()` |

Rules live in `reflex-rules/` as standard Reflex YAML. They're portable — use them with Claude Code, Cursor, Codex, or any runtime with a Reflex adapter. See [@fozikio/reflex](https://github.com/Fozikio/reflex) for the full rule format and tier enforcement.

**Claude Code users** also get platform-specific hooks (in `hooks/`) for telemetry, session lifecycle, and project board gating. These are runtime adapters, not rules — they handle side effects that the declarative rule format doesn't cover.

**To customize:** Edit the YAML rule files directly, or set `allow_disable: true` and disable them via Reflex config.

### Skills

Skills are invocable workflows that agents can use via `/skill-name`.

| Skill | When to Use | What It Provides |
|-------|-------------|-----------------|
| `cortex-memory` | Query, record, and review work | Full memory workflow — query/observe patterns, belief tracking, memory-grounded code review, session patterns |

### Agents

| Agent | Description |
|-------|-------------|
| `cortex-researcher` | Deep research agent that queries cortex before external sources, observes novel findings back into memory |

### How Auto-Install Works

1. `fozikio init` reads `fozikio.json` from the package root
2. Copies hooks, skills, and Reflex rules into the target workspace
3. Missing source files are skipped with a warning — init never fails due to missing assets

## Built-in Capabilities (v1.0.0+)

As of v1.0.0, all 60 cognitive tools are built into cortex-engine core — no separate plugin installs needed. Previously these were separate `@fozikio/tools-*` packages; they've been absorbed into the engine.

| Capability | Tools |
|-----------|-------|
| **Memory** | `observe`, `query`, `recall`, `wander`, `wonder`, `forget`, `retrieve`, `context`, `feedback`, `query_cross`, `federated_query` |
| **Beliefs & Reasoning** | `believe`, `belief`, `contradict`, `speculate`, `validate`, `predict` |
| **Threads** | `thread_create`, `thread_update`, `thread_resolve`, `threads_list` |
| **Journaling** | `journal_write`, `journal_read` |
| **Identity** | `evolve`, `evolution_list` |
| **Social** | `social_read`, `social_update`, `social_draft`, `social_score` |
| **Graph** | `neighbors`, `suggest_links`, `suggest_tags`, `link`, `graph_report` |
| **Maintenance** | `dream`, `digest`, `reflect`, `abstract`, `find_duplicates`, `retrieval_audit`, `consolidation_status` |
| **Vitals** | `vitals_get`, `vitals_set`, `sleep_pressure` |
| **Reasoning** | `surface`, `ruminate`, `notice`, `intention`, `resolve` |
| **Content** | `content_create`, `content_list`, `content_update` |
| **Ops** | `ops_append`, `ops_query`, `ops_update` |
| **Goals** | `goal_set` |
| **Agents** | `agent_invoke` |
| **Stats** | `stats`, `query_explain` |

The plugin system is still available for custom extensions — see [Plugin Docs](https://www.fozikio.com/products/plugins/).

## Documentation

- **In-repo docs**:
  - [Quick Start](docs/quick-start.md) — 5-minute setup
  - [Storage backends](docs/storage-backends.md) — SQLite vs Firestore vs JSON, migration paths
  - [Concurrency model](docs/concurrency.md) — `withTransaction` contract, single-process invariant, SQLite vs Firestore semantics
  - [Tools reference](docs/tools-reference.md) — all 60 tools by category with when-to-use guidance (auto-generated)
  - [Multi-agent design](docs/multi-agent-design.md) — namespace isolation, bridges, federation
  - [Design specs](docs/superpowers/specs/) — design documents from the v1.2.0 audit-driven refactor
  - [Agent-first setup](docs/agent-first-setup.md) — Workspace initialization walkthrough
- **[Discussions](https://github.com/Fozikio/cortex-engine/discussions)** — Ask questions, share what you've built
- **[Contributing](https://github.com/Fozikio/.github/blob/main/CONTRIBUTING.md)** — How to contribute
- **[Project Board](https://github.com/orgs/Fozikio/projects/2)** — Roadmap and active work
- **[Security](https://github.com/Fozikio/.github/blob/main/SECURITY.md)** — Report vulnerabilities

## Community

- [r/Fozikio](https://www.reddit.com/r/Fozikio/) — Project subreddit
- [GitHub Discussions](https://github.com/Fozikio/cortex-engine/discussions) — Questions, feedback, show what you've built
- ["I built 44 MCP tools for my cognitive system"](https://reddit.com/r/mcp/comments/1rno9pu/) — r/mcp deep dive (84 upvotes, 27 comments)
- ["Gave my agent a subconscious"](https://reddit.com/r/clawdbot/comments/1rtvex3/) — r/clawdbot walkthrough (22 upvotes, 34 comments)

## Related Projects

- [@fozikio/reflex](https://github.com/Fozikio/reflex) — Portable safety guardrails for agents. Rules as data, not code.
- [sigil](https://github.com/Fozikio/sigil) — Agent control surface. Signals and gestures, not conversations.
- [fozikio.com](https://www.fozikio.com) — Documentation and guides

## License

MIT — see [LICENSE](LICENSE)

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