Vault Structure

A Context Nest vault is a directory containing Markdown documents, configuration, and version history.

Structured layout (default)

my-vault/
├── CONTEXT.md              # Vault-level system prompt for AI agents
├── context.yaml            # Machine-readable index (auto-generated)
├── nodes/                  # Knowledge documents
│   ├── INDEX.md            # Auto-generated folder index
│   ├── architecture.md
│   └── api-reference.md
├── sources/                # Source nodes (live data instructions)
│   ├── INDEX.md
│   └── current-sprint.md
├── packs/                  # Context packs (YAML)
│   └── engineering-essentials.yml
├── .context/               # Configuration
│   └── config.yaml
└── .versions/              # Version history (auto-managed)
    ├── context_history.yaml
    └── nodes/
        └── architecture/
            └── history.yaml

Key files

CONTEXT.md

The vault-level system prompt. AI agents read this first to understand the vault's purpose, structure, and how to interact with it.

context.yaml

Machine-readable index auto-generated by the CLI. Contains:

• List of all published documents with metadata
• Relationship graph (context links, backlinks, dependencies)
• Hub documents (highest inbound reference count)
• External dependencies (MCP servers, tools required by source nodes)

config.yaml

Vault configuration in .context/config.yaml:

name: "My Project"
namespace: "my-project"
layout: structured
federation: none

Obsidian layout

For Obsidian users, vaults can use a flat structure without the nodes/ / sources/ separation:

my-vault/
├── CONTEXT.md
├── context.yaml
├── architecture.md
├── api-reference.md
├── .context/
│   └── config.yaml
└── .versions/