--- title: Agent Manifest description: "Documentation structure and navigation guide for AI agents consuming Matrix docs." --- > **For AI agents:** the complete documentation index is at [llms.txt](/llms.txt). Append `.md` to any page URL for its markdown version. This page describes the Matrix documentation structure for AI agents and LLMs. ## Repository Overview Matrix is the cognition and UX layer on Paxeer Network. It turns natural language into typed, inspectable, replayable agent execution across two rails: - **Neo**: Conversational tool-calling agent for reversible work - **MCL**: Rigorous rail for monetary/irreversible work (NL → Intent IR → Plan → Walk) ## Documentation Structure ### Entry Points (read these first) 1. [Introduction](/introduction) - Mental model, two rails, full stack overview 2. [Quickstart](/quickstart) - Build, compile first intent, run daemon 3. [Core Concepts](/concepts) - Core concepts: intents, frames, verbs, cortex, replay 4. [Glossary](/glossary) - All Matrix terms defined ### Key Subsystems **Core Modules** (see [Architecture](/developer/architecture) for the layered model): - `mcl/` - Compiler: prose → Intent IR → PlanTree - `cortex/` - Per-actor typed memory graph (Pebble DB, journal, snapshots) - `executor/` - Plan walker, lifecycle machine, MCP dispatch - `neo/` - Conversational agent, tool-calling loop - `gateway/` - Metered LLM proxy, PAX credit ledger - `router/` - JWT verify, Fly Machine wake, reverse proxy - `deus/` - Agent-service marketplace - `layerx/` - Settlement fabric, custody spine - `chronos/` - Agent scheduler, wake system - `tachyon/` - Solidity/EVM engine - `uwac/` - Universal Web Agent Connector ### File Format All documentation uses `.mdx` (Markdown + JSX components). Frontmatter includes: - `title`: Page title - `description`: One-line summary Common MDX components: - `` - Multi-column layout - `` - Navigation cards - ``, ``, `` - Callout boxes - `` / `` - Numbered procedures - `` / `` - Collapsible sections ### Navigation The `docs.json` file defines the navigation structure: - 6 tabs: Documentation, Developer, API Reference, MCP, Reference, FAQ - Each tab has groups of related pages - Reference section has deep subsystem docs (cortex, mcl, neo, chronos, tachyon, deus, layerx, skills, standards) ### API Reference - [Overview](/api-reference/overview) - Service table, auth patterns - [Daemon](/api-reference/daemon) - HTTP + SSE surface (/chat, /events, /messages, /intents) - [Gateway](/api-reference/gateway) - Metered LLM proxy, rate card - [Router](/api-reference/router) - JWT verify, wake, proxy - [Chronos](/api-reference/chronos) - Scheduler API - [Deus](/api-reference/deus) - Marketplace API - [LayerX](/api-reference/layerx) - Settlement API - [UWAC](/api-reference/uwac) - OAuth vault API - [Tachyon](/api-reference/tachyon) - EVM engine API - [CLI](/api-reference/cli) - CLI reference ### Deep Reference Each subsystem has an `overview.mdx` plus detailed pages: - `reference/cortex/` - 13 pages (store, journal, taxonomy, write API, find, context bundle, embedder, edges, snapshots, salience, attest, scope, replay) - `reference/mcl/` - 8 pages (compiler pipeline, intent IR, envelope, matrixscript, skill authoring, mclc CLI, LLM client) - `reference/neo/` - 10 pages (control loop, memory system, recall lane, conversation store, core execute, writeback, tool surface, LLM client, config) - `reference/chronos/` - 10 pages (architecture, API, auth, config, data model, dispatch worker, schedule engine, tool surface, wake delivery) - `reference/tachyon/` - 17 pages (daemon, API server, RPC server, MCP server, compiler, engine, ABI encoder, EVM client, deployer, wallet, registry, simulate, tester, chains, config, types) - `reference/deus/` - 6 pages (service entrypoints, discovery, receipts, chain access, hosting, contracts) - `reference/layerx/` - 3 pages (daemon, settlement contracts, forge integration) - `reference/skills/` - 5 pages (agent engineering, planning, react, brand, tooling) - `reference/standards/` - 5 pages (contribution, testing, patterns, lifecycle, security) ### Cross-References Pages link to each other using: - Markdown links: `[text](/path/to/page)` - Card components: `` All internal links resolve to existing `.mdx` files except: - `faq/security.mdx` references `SECURITY.md` which does not exist ### Build & Deploy - Source: `https://github.com/dev-paxeer/matrix-docs` - Platform: Jamdesk documentation platform - Build: `jamdesk build` (generates static site) - Deploy: `jamdesk deploy` (publishes to docs.matrixmcl.com) ## Agent Consumption For LLM/agent consumption: 1. Read [LLM Index](/llms) for a structured index with descriptions 2. Read [Sitemap](/sitemap) for a flat list of all paths 3. Read individual `.mdx` files, stripping JSX components to extract text 4. The [Glossary](/glossary) is pure markdown tables — easiest to parse ## Known Issues 1. `README.md` is Jamdesk template boilerplate (not Matrix-specific) 2. FAQ pages use `` only — no markdown headings for structure 3. `api-reference/request-response-examples.mdx` and `api-reference/openapi-example.mdx` are Jamdesk template demos (not Matrix content) 4. `mcp/writing-a-tool-bridge.mdx` has zero markdown headings 5. `faq/security.mdx` references non-existent `SECURITY.md` 6. API reference pages lack response body shapes and error examples 7. `user-guide/skills.mdx` is thin (216 words, 2 headings) ## Recommendations for Agents 1. Start with [Introduction](/introduction), [Core Concepts](/concepts), [Glossary](/glossary) for mental model 2. Use [Quickstart](/quickstart) for build/run instructions 3. For subsystem details, read the `overview.mdx` first, then drill into specific pages 4. Strip MDX components (``, ``, ``, etc.) to extract plain text 5. All code examples are in standard markdown code blocks — parse normally 6. Cross-references use absolute paths from root (`/path/to/page`)