mstack-init

A setup skill that creates the standard folder structure for a new research paper, project, or study. MStack is the project template, with separate folders for the paper, data, code, output, and stored project memory.

In plain words
What is it for?
Use it to start a paper with a short name and choose LaTeX or Quarto, a format that combines formatted text with executable analysis.
Why use it?
It gives later paper-writing tools the paths and configuration they expect, while preventing projects from being nested inside one another.

Skill for Claude CodeCodex

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/matthewdigiuseppe/mstack/mstack-init
Any agent
npx skills add matthewdigiuseppe/MStack --skill mstack-init
Clone the repo
git clone --depth 1 https://github.com/matthewdigiuseppe/MStack

Made for: Claude Code, Codex.

Per session 77 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 711 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
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 $0.00077 $0.00711
Opus 5 $0.00039 $0.00356
Sonnet 5 $0.00015 $0.00142
Haiku 4.5 $0.00008 $0.00071

Measured 2d ago against content hash 253772ba4d09, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

mstack-init 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.

skills/mstack-init/SKILL.md · 59 lines

How it starts

The opening of the file, as written. The whole thing — 59 lines — stays where its author put it; the contents beside it link to each section on GitHub.

/mstack:mstack-init

Stage: setup Voice: scaffolder

When to invoke

Starting a new paper. Every other MStack skill assumes the folder layout this skill creates; run it once per paper, in the directory where the paper folder should live.

Argument

$ARGUMENTS — a short slug for the paper (e.g. tariffs-aid), optionally followed by --quarto for a Quarto main file instead of LaTeX. If no slug is given, ask for one (lowercase, hyphens, no spaces).

Procedure

  1. Refuse to nest. If the current directory (or an ancestor) already contains .mstack/, stop — a paper folder inside a paper folder breaks every path convention. Tell the user to cd out first.

  2. Run the bundled script. The plugin root is available as ${CLAUDE_PLUGIN_ROOT}:

    bash "${CLAUDE_PLUGIN_ROOT}/bin/mstack-init" <short-name> [--quarto]
    
  3. Fallback (script missing or no bash): replicate it manually —

    • Copy ${CLAUDE_PLUGIN_ROOT}/templates/paper-folder to ./<short-name> (preserve hidden files).
    • Stamp short_name: "<short-name>" into .mstack/config.yaml.
    • If --quarto: replace paper/main.tex with a main.qmd that {{< include >}}s the section files as .qmd, and set format: "quarto" in config.
  4. Verify the tree exists (.mstack/config.yaml, paper/, data/raw/, code/, output/).

  5. Hand off. Tell the user to fill in .mstack/config.yaml (title, authors, target journals, voice.writing_style if they have a style skill installed), then start with /mstack:research-question or /mstack:idea-shotgun.

Outputs

  • ./<short-name>/ — the full paper scaffold.
  • Summary block: created path, format (latex/quarto), next steps.

Anti-patterns to refuse

  • Scaffolding over an existing folder. If ./<short-name> exists, stop; never merge into it.
  • Skipping config. A scaffold with an empty config still works, but remind the user once — several skills read target_journals and voice.*.

When to call other skills

Read the full file on GitHub · 59 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 · 59 lines · 77 tokens per session scan A 253772ba4d09

Subscribe to this mod's changes

mstack-init is a skill published in the GitHub repository matthewdigiuseppe/MStack (14 stars, last pushed 5d ago), licensed MIT. It adds 77 tokens to every session and 711 once invoked, about $0.0004 per session on Opus 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 2026-08-30.

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