Context System
Cortex injects context at the start of each new session so Claude understands your vault before you ask your first question. Nothing extra is injected on subsequent turns — those use session resumption (--resume), which is far cheaper.
1. System Orientation
Automatically injected at every new session — no configuration needed. Tells Claude what Cortex is, that it's operating inside Obsidian, what tools it has, and how to interact with the UI.
2. Vault Tree
A folder and file name overview of your vault. Only names are listed — no file contents are read. Hidden files and folders (starting with .) are skipped.
Configure depth in Settings → Cortex → Vault tree depth:
| Setting | What Claude sees |
|---|---|
| Off | No vault tree |
| 1 level | Root-level folders and files only |
| 2 levels | Root + one sublevel |
| 3 levels (default) | Root + two sublevels |
| Unlimited | Full tree at any depth |
Deeper trees give Claude better spatial awareness of large vaults but cost more tokens per session start. For most vaults, 3 levels is a good balance.
3. Context File (Persistent Memory)
A markdown file injected at the start of every session. Default path: _claude-context.md at your vault root. This is Claude's persistent memory — it survives across sessions and syncs with your vault.
Seed it manually with your vault conventions:
# My Vault Context
## Conventions
- Meeting notes go in 02_Calendar/YYYY-MM-DD format
- Projects live in 06_Spaces/Projects/
- Use #status/active and #status/done tags
## Current focus
Working on Q2 planning. Key notes: [[Q2 Goals]], [[Team Roster]]The context file path is configurable in Settings → Cortex.
4. Active Note
The path of the currently open note is prepended to every message — e.g. [Active note: 06_Spaces/Projects/Alpha.md]. Claude always knows which note you're looking at.
Split-pane awareness: When you have multiple notes open side by side, Cortex injects all visible file paths instead — e.g. [Open in split view: Notes/A.md | Projects/B.md]. Toggle in Settings → Inject split-pane files as context.
5. Per-note Frontmatter Context
Add Cortex properties to any note's frontmatter to control how Claude treats it.
| Property | Value | Effect |
|---|---|---|
cortex-context | always | Full note content injected at every session start |
cortex-instructions | any string | Instruction injected telling Claude how to treat this file |
Pin a note to every session (e.g. a project brief or style guide):
---
cortex-context: always
---Give Claude standing instructions for a file:
---
cortex-instructions: "Always write in present tense and keep bullets under 10 words."
---Both together:
---
cortex-context: always
cortex-instructions: "This is the team writing guide — apply its rules to any note you edit."
---Partial file protection
You can use cortex-instructions to tell Claude not to modify a file — e.g. "Read for reference only. Do not edit." This works well in practice but is convention, not enforcement. For truly critical files, keep a backup or use git history.
6. Autonomous Memory
When Autonomous memory is on (default), Claude is instructed to actively maintain the context file as it learns about your vault — naming conventions, ongoing projects, your preferences. Claude updates the file directly using its file-editing tools; you can inspect and edit it at any time.
Disable in Settings → Cortex → Autonomous memory if you prefer to manage it manually, or if your vault is shared.
Two kinds of memory
Session memory (--resume) | Autonomous memory (context file) | |
|---|---|---|
| What | Full conversation history | Key facts Claude chose to remember |
| How long | Until the Claude Code session expires | Permanent (until you edit or delete) |
| Cross-machine | No — stored in ~/.claude/ locally | Yes — travels with vault sync |
| Size | 10KB–several MB per session (plain JSON lines) | As small as you keep it |
| Inspectable | No | Yes — it's a markdown file |
Cross-machine sessions
Session files are keyed to the vault's absolute path. Resuming a session from another machine requires the same absolute path AND the session file present on that machine — generally not practical. Use the context file for cross-machine continuity.