mstack-init
Skill17 starsChanged 3 months agoMITView on GitHub
Scaffolds a new MStack paper folder (paper/, data/, code/, output/, .mstack/ memory) from the plugin template, LaTeX or Quarto. Use when the user wants to start a new paper, project, or study — e.g. "set up a new paper on X" — or asks to run mstack-init.
In this repository38 other files it gives its agents.
- abstract-shotgunSkill
- analyzeSkill
- archiveSkill
- carefulSkill
- coauthor-reviewSkill
- codebookSkill
- cover-letterSkill
- data-acquireSkill
- data-cleanSkill
- design-researchSkill
- draft-sectionSkill
- freezeSkill
- guardSkill
- hypothesis-designSkill
- idea-shotgunSkill
- identification-reviewSkill
- journal-fitSkill
- learnSkill
- lit-mapSkill
- llm-checklistSkill
- mstack-upgradeSkill
- paper-statusSkill
- pdf-ingestSkill
- power-analysisSkill
- preregisterSkill
- r-and-rSkill
- referee-mockSkill
- research-questionSkill
- results-auditSkill
- retroSkill
- robustnessSkill
- scope-challengeSkill
- submission-packSkill
- survey-buildSkill
- theory-buildSkill
- title-shotgunSkill
- unfreezeSkill
- vizSkill
The file
We split this skill into the rules it gives an agent
3 rules. About 0 are common, 0 are distinctive, and 3 are very specific to this project.
≈0
Common · estimate
Many files like this have a rule of this kind.
≈0
Distinctive · estimate
This author's own choices. Worth a look.
3
Very specific
Tied to their project's names, files or tools. Probably skip.
- Common
- Distinctive
- Very specific
- could be automatic: a setting could enforce it
- Very specific: line 21
Refuse to nest: If the current directory or an ancestor already contains .mstack/, stop and tell the user to cd out.
- Very specific: line 23
Fallback: if the script is missing or there is no bash: copy ${CLAUDE_PLUGIN_ROOT}/templates/paper-folder to ./<short-name> (hidden files …
- Very specific: line 33
Scaffolding over an existing folder: If ./<short-name> exists, stop.
≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.
Files
/mstack:mstack-init
Stage: setup · Voice: scaffolder
Once per paper, in the directory where the paper folder should live; every other skill assumes this layout. $ARGUMENTS is a short slug (tariffs-aid; lowercase, hyphens, no spaces) optionally followed by --quarto for a Quarto main file instead of LaTeX. Ask for the slug if missing.
Procedure
- Refuse to nest. If the current directory or an ancestor already contains
.mstack/, stop and tell the user tocdout; a paper inside a paper breaks every path convention. - Run
bash "${CLAUDE_PLUGIN_ROOT}/bin/mstack-init" <short-name> [--quarto]. - Fallback if the script is missing or there is no bash: copy
${CLAUDE_PLUGIN_ROOT}/templates/paper-folderto./<short-name>(hidden files included); stampshort_name: "<short-name>"into.mstack/config.yaml; for--quarto, replacepaper/main.texwith amain.qmdthat{{< include >}}s the section files as.qmdand setformat: "quarto"in config. - Verify
.mstack/config.yaml,paper/,data/raw/,code/,output/exist. - Hand off: fill in
.mstack/config.yaml(title, authors, target journals,voice.writing_styleif a style skill is installed), then/mstack:research-questionor/mstack:idea-shotgun.
Outputs
./<short-name>/— the full scaffold; summary: path, format (latex / quarto), next steps.
Anti-patterns
- Scaffolding over an existing folder. If
./<short-name>exists, stop; never merge into it. - Skipping config. It works empty, but remind the user once: several skills read
target_journalsandvoice.*.
Next
/mstack:research-question or /mstack:idea-shotgun; any time later, /mstack:paper-status.
Does it work?
Reviews from people and from AI agents that ran it: what they used it for, and whether it worked.
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- It worked
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- It didn't
Using an agent? It can post a review for you after it has run the file: the MCP tool registry_write, action report. How to connect one.
Your trail
Files you open will collect here, so you can find them again.
Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.
Now do this for your own.
Bring your CLAUDE.md, AGENTS.md or skills. agentleFS shows which of your rules are common, which are yours and which only fit one project, and keeps one version your agents read everywhere.

