ReactiveDynamics.jl: Instructions file for Claude Code

CLAUDE.md

ReactiveDynamics.jl CLAUDE.md is an instructions file for Claude Code from Merck/ReactiveDynamics.jl. It costs 3,491 tokens per session, scanned A, original, MIT.

Project-specific instructions for working on ReactiveDynamics.jl, a Julia engine for modelling timed, resource-limited processes and their costs or rewards. They explain the project structure, durable specifications, and development and testing practices.

In plain words
What is it for?
Use them when exploring, changing, building, or testing the ReactiveDynamics.jl repository and its agent-related layer.
Why use it?
They give a coding agent the background needed to avoid confusing this system with a chemical reaction model. They also point it to the right files and require checks such as re-confirming changing line references.

Instructions file for Claude Code

Written for Claude Code: the file is CLAUDE.md. Also seen: mentions CLAUDE.md.

This is Merck/ReactiveDynamics.jl's own configuration. It tells Claude Code how to work on ReactiveDynamics.jl 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 ReactiveDynamics.jl configures →

Reuse

Borrowing it

Nothing to install: this file belongs to Merck/ReactiveDynamics.jl. 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/Merck/ReactiveDynamics.jl/main/CLAUDE.md
Clone the repo
git clone --depth 1 https://github.com/Merck/ReactiveDynamics.jl

Made for: Claude Code.

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Per session 3,491 This file is loaded in full into every session.
When invoked 3,491 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 $0.03491 $0.03491
Opus 5.5 $0.01396 $0.01396
Sonnet 5.5 $0.00698 $0.00698
Haiku 4.5 $0.00349 $0.00349

Measured 2d ago against content hash fb13c8bd3b85, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

ReactiveDynamics.jl CLAUDE.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 2d ago.

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.

CLAUDE.md · 64 lines

How it starts

The opening of the file, as written. The whole thing — 64 lines — stays where its author put it; the contents beside it link to each section on GitHub.

CLAUDE.md — ReactiveDynamics.jl agent guide

Agent-facing orientation for the ref-agents branch. Re-verify any file:line before acting — line numbers drift; grep to confirm.

What this project is

ReactiveDynamics.jl (RD) is a timed, stochastic, resource-constrained Petri net / discrete-event engine for system-dynamics-style modeling of business / R&D processes (budgeting, ledgers, what-if, rNPV) — NOT a chemical reaction network, despite the Catalyst-derived DSL surface. A transition is a stateful recipe that spawns in-flight instances at a Poisson rate, occupies shared finite resource pools (places) over a cycle time, and completes with a terminal probability-of-success that emits RHS products. Resources carry a modality governing allocation (:nonblock/:conserved/:rate), and a cost/reward/valuation ledger accumulates into a per-step log. Structured/agentic tokens are first-class entities (a "project" is an agent with attributes, custom behavior, and history) that can be instantiated, selected by predicate, advanced through lifecycle phases, and audited per-program. RD is part of the DyVE family and sits ON TOP of AlgebraicAgents.jl (AA): a ReactionNetworkProblem IS an AA @aagent, so a network is a node in a larger heterogeneous AA hierarchy.

Where the durable spec lives

The durable engineering artifacts live under top-level spec/, kept separate from docs/ — which is reserved for the Documenter.jl static-pages site (docs/make.jl, docs/src/, generated docs/build/). Do not put spec material in docs/.

spec/STATUS.md is the single entry point — start there. It carries the authoritative catalog of every durable artifact (CONTRACT_DRAFT, adr/, PR_DRAFT, DOCS_CHARTER, INVENTORY, the retired/archived docs) so this guide need not duplicate it. The three you touch most:

  • spec/STATUS.md — "what is the state, what is left." The dashboard: feature→commit table, test tally, deferred items with gates.
  • spec/CONTRACT_DRAFT.md — the normative operational-semantics spec (§1–§15). The durable spine: what the engine must do.
  • spec/INVENTORY.md — the current-source map (module map, public-API audit, static store, stepping trace, AA touchpoints): where it lives in the source.
  • spec/adr/ — Architecture Decision Records (append-only), status table in spec/adr/README.md. To change a decision, add a new ADR; do not rewrite history.

Read the full file on GitHub · 64 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. 2d ago First seen · 64 lines · 3,491 tokens per session scan A fb13c8bd3b85

Subscribe to this mod's changes

ReactiveDynamics.jl CLAUDE.md is an instructions file published in the GitHub repository Merck/ReactiveDynamics.jl (17 stars, last pushed 27d ago), licensed MIT. It adds 3,491 tokens to every session, about $0.0140 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 2026-11-07.

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