---
title: CLI Reference
description: "The Matrix command-line surfaces — mclc, mcl-execute, mcl-tools, mcl-validate, cortex-shell, deusctl, and neo — and what each subcommand does."
---

> **For AI agents:** the complete documentation index is at [llms.txt](/llms.txt). Append `.md` to any page URL for its markdown version.

Matrix ships several CLIs built by `make install` into `./bin`. They share flags like `-cortex-root`, `-manifest`, and `-skills-root`.

## `mclc` — the compiler

| Subcommand | Purpose |
| --- | --- |
| `compile` | Compile prose + a skill + a verb into an Intent Frame. |
| `validate` | Strict validation of a `SKILL.mtx`. |
| `hash` | Compute the canonical AST digest. |
| `parse` | Parse and dump the AST. |

```bash
./bin/mclc compile -skill skills/writing-plans/SKILL.mtx \
  -prose "Build a deployment pipeline" -verb build [-dry-run]
```

## `mcl-execute` — the runtime

| Subcommand | Purpose |
| --- | --- |
| `walk` | Compile an intent, synthesize a PlanTree, and walk it to completion. |
| `classify` | Run the materiality classifier on an intent. |
| `loader` | Load and inspect an agent manifest + its skills. |
| `daemon` | Run the per-user HTTP + SSE daemon. |

```bash
./bin/mcl-execute walk -prose "Summarise the README" \
  -manifest agents/default.json -cortex-root ./runs/dev-cortex -skills-root ./skills
```

## `mcl-tools` — MCP tool inspection

| Subcommand | Purpose |
| --- | --- |
| `verify` | Verify a manifest's tool bijection (declared == discovered). |
| `list` | List tools exposed by the manifest's MCP servers. |
| `describe` | Show a tool's schema. |
| `call` | Invoke a tool directly. |

## `mcl-validate`

Validates a single `SKILL.mtx`. The `mtx-corpus` CI job runs this across the whole corpus on every PR.

```bash
./bin/mcl-validate skills/<slug>/SKILL.mtx
```

## `cortex-shell`

Inspect and maintain a cortex store. The load-bearing command is the replay verifier:

```bash
cortex-shell rebuild -verify-only   # drop derived, rebuild, assert byte-identical OverallRoot
```

## `deusctl` & `neo`

- **`deusctl`** — operate the Deus marketplace control plane (register/publish services, manage deployments).
- **`neo`** — run the Neo conversational agent locally (CLI reporter → stdout/stderr).

<Card title="MCL & skill authoring" icon="diagram-project" href="/developer/mcl">
  Author the skills these CLIs compile.
</Card>