crystalline: Instructions file for Codex

AGENTS.md

crystalline AGENTS.md is an instructions file for Codex, OpenCode from jordiboehme/crystalline. It costs 6,659 tokens per session, scanned A, original, MPL-2.0.

A repository instruction file describing Crystalline, a local-first knowledge system for humans and AI agents. It stores accumulated information and experience in Markdown files or a database, with a search index used as a temporary derived layer.

In plain words
What is it for?
Use it when working on Crystalline's knowledge storage, agent onboarding, routing prompts, search layer, or user-facing terminology.
Why use it?
It gives agents persistent project knowledge so they do not have to start each session without the information and experience gathered earlier.

Instructions file for CodexOpenCode

Written for Codex and OpenCode: the file is AGENTS.md. Also seen: mentions subagents.

This is jordiboehme/crystalline's own configuration. It tells Codex and OpenCode how to work on crystalline itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything crystalline configures →

Reuse

Borrowing it

Nothing to install: this file belongs to jordiboehme/crystalline. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/jordiboehme/crystalline/main/AGENTS.md
Clone the repo
git clone --depth 1 https://github.com/jordiboehme/crystalline

Made for: Codex, OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

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README.md
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Your own site
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Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

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Per session 6,659 This file is loaded in full into every session.
When invoked 6,659 The same file — it is already loaded in full.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.06659 $0.06659
Opus 5.5 $0.02664 $0.02664
Sonnet 5.5 $0.01332 $0.01332
Haiku 4.5 $0.00666 $0.00666

Measured yesterday against content hash 626772a55820, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

crystalline AGENTS.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

AGENTS.md · 101 lines

How it starts

The opening of the file, as written. The whole thing — 101 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Crystalline

Local-first knowledge management for humans and AI agents. Every Domain has exactly one source of truth: by default Markdown files (Engrams) on disk, or, for a virtual domain, the database itself. The search index is always a disposable derived layer; an MCP server and CLI sit on top.

Purpose

Crystalline gives an AI agent the capability to learn and evolve instead of starting from zero in every session. An agent is onboarded via a generated routing prompt, taught information through curated domains and stores its learnings and experiences as engrams while it works - becoming a useful and productive peer over time. All user-facing language (README, skills, MCP tool descriptions, routing prompt) is framed around onboarding, teaching, learning and experience rather than notes or documents.

Positioning follows the psychology concept of fluid vs crystallized intelligence: a language model is fluid intelligence (reasons in the moment, keeps nothing), Crystalline is the crystalline intelligence an agent accumulates and keeps, and the web UI (Fluid) is where the two meet. Describe the product as "crystalline intelligence"; the agent-facing phrase avoids the Crystalline/crystalline doubling and reads "Crystalline is your crystallized intelligence across sessions". Never describe it as "crystalline memory" or a memory tool.

Vocabulary

  • Domain - a registered folder of knowledge with a mandatory MANIFEST.md at its root, used for routing
  • Engram - one markdown file holding a unit of knowledge, with YAML frontmatter (OKF compatible)
  • Address scheme: crystalline://<domain>/<permalink>

Workspace

Cargo workspace, Rust edition 2024, pinned toolchain in rust-toolchain.toml.

  • crates/core (crystalline-core) - format layer: parser, emitter, schema, verify, prompt. Must never depend on async runtimes, databases or ML crates
  • crates/index (crystalline-index) - Store trait, embedded database backend, sync engine, search, embeddings. The local embedding model and the contradiction check's NLI model run on Metal on Apple Silicon Macs (candle's metal feature, enabled for aarch64-apple-darwin only) with a CPU fallback, and on the CPU everywhere else (src/device.rs, one device pick per model load)
  • crates/remote (crystalline-remote) - GitHub-backed team collaboration plumbing and the client for connected Crystalline servers (credentials, sources, connection, cache): the forge-neutral Provider trait, the plain-text merge engine and the on-disk origin state. Git is never invoked; everything goes through the GitHub APIs
  • crates/identity (crystalline-identity) - accounts, roles, domain access, joins and scope
  • crates/engine (crystalline-engine) - the shared engine, review-mode overlay, origins, co-editing sessions
  • crates/rest (crystalline-rest) - the JSON API, sign-in and the co-editing socket
  • crates/service (crystalline-service) - single-instance daemon, MCP server, control protocol; the facade the CLI and the integration tests reach everything through
  • crates/cli (crystalline) - the single user-facing binary

Read the full file on GitHub · 101 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. yesterday Changed · +4 lines · +529 tokens per session 626772a55820
  2. 5d ago Changed · +5 lines · +1,071 tokens per session 612676ba3450
  3. 11d ago Changed · +2 lines · +165 tokens per session 7efd717a442e
  4. 13d ago Changed · +12 tokens per session a4d2766fb26b
  5. 14d ago Changed · +2 lines · +326 tokens per session 2f13f6a61b40
  6. 15d ago Changed · +1 lines · +208 tokens per session 7773deeff3bc
  7. 19d ago Changed · +1 lines · +44 tokens per session cc2e9bb4c1be
  8. 21d ago Changed · +16 tokens per session eec349a1c40a
  9. 22d ago First seen · 86 lines · 4,288 tokens per session scan A 8901ffd8a329

Subscribe to this mod's changes

crystalline AGENTS.md is an instructions file published in the GitHub repository jordiboehme/crystalline (17 stars, last pushed 2d ago), licensed MPL-2.0. It adds 6,659 tokens to every session, about $0.0266 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-10-06.

Related

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