write-plan - SKILL.md Agent Skill

name: write-plan description: Use when a research design spec exists and the user is ready to translate it into a concrete implementation plan with phased tasks, artifacts, and verification criteria. Produces a research execution plan organized in canonical research phases — collection, preparation, analysis, robustness, writing, submission.

Write Plan

Overview

This skill writes a detailed, research-structured implementation plan from an approved design spec. It begins by invoking academic-baseline as the standing policy layer for the planning session. The plan is organized in research phases — not software phases — and every task has an expected artifact, verification criterion, and explicit skill routing. replication-driven-research is invoked as a hard constraint: every task must produce a versionable artifact and fit into an end-to-end reproducible pipeline.

When to Use

An approved design spec exists in docs/superpapers/specs/
User says "now write the plan", "let's plan this out", or "next step"
Transitioning from brainstorm to implementation
Planning a revision round after reviewer feedback

Prerequisites

A spec in docs/superpapers/specs/YYYY-MM-DD-<topic>-design.md, written and approved via brainstorm
User has confirmed they want to proceed from the spec to a concrete plan

Mandatory Steps

Invoke academic-baseline first. This resolves CLAUDE.superpapers.md via the walk-up Read (current working directory, then parent directories) and carries its settings and principles through the entire planning step.
Read the design spec in full. Understand every decision the brainstorm made — research question, identification strategy, data sources, models, robustness plan, submission target.
Decompose into tasks following the canonical research phases (see below). Aim for bite-sized tasks — 10 to 30 minutes of work each. If a task is a full day of work, split it.
For every task, specify all task-template fields (see template below). No placeholders. Every field filled explicitly.
Map dependencies. Later phases depend on earlier phases. Within a phase, tasks may be parallel or sequential — mark explicitly.
Assign skills deliberately. The Skills involved field is mandatory routing metadata, not decoration. Include academic-baseline on every task as the standing foundation, then add the domain skills actually needed. Any task involving target journal selection, author instructions, formatting, templates, blinding, cover letters, checklists, or submission portals must include journal-guidelines; if the outlet is not fixed yet, include journal-selection before journal-guidelines.
Apply replication-driven-research as a constraint. Every task must produce a versionable artifact. Every stochastic script must fix the seed. Every output must feed into an end-to-end pipeline.
Write the plan to docs/superpapers/plans/YYYY-MM-DD-<topic>-plan.md in English. The plan is a plugin artifact like the spec — English for consistency.
Self-review for coverage (every spec requirement has a task?), placeholders, name or type consistency across tasks, skill routing completeness, and scope fit (can this be one plan or does it need splitting?).
Offer execution options. Present execute-plan as the next step, with the choice between subagent-driven execution and inline execution.

Canonical Research Phases

The plan is organized in these phases — not software phases. Each phase has tasks; each task has an expected artifact and a verification step.

1. Literature

Full literature review that grounds the paper and positions it against existing work. Tasks: invoke literature-search in full mode (all Mandatory Steps, including the target-journal bias) to curate 15-30 key references; populate paper/references.bib via citation-management; produce a synthesized literature notes document (e.g., docs/superpapers/literature-notes.md) that will feed the Introduction and Literature Review sections during writing. The brief gap check run inside brainstorm is not a substitute — this phase is the substantive literature engagement. Verification: bibliography populated and DOI-verified, notes cover (a) state of the field, (b) methods and data typical in the area, (c) papers this work positions against, (d) recent target-journal publications. Skills involved: academic-baseline, literature-search, citation-management.

2. Collection

Fetch raw data. Tasks: identify sources (via data-collection), implement collection scripts, save to data/raw/, update data/manifest.md. Verification: raw files exist, manifest entries present.

3. Preparation

Clean and merge. Tasks: cleaning scripts, merge logic, derived variables, sample selection rules. Verification: processed data exists in data/processed/, sample selection documented.

4. Exploratory Analysis

Descriptive statistics, visualizations, data quality checks. Tasks: tab_descriptives.tex, fig_trends.pdf, anomaly detection. Verification: outputs exist; a reviewer can read them before the main analysis.

5. Main Analysis

The specified model from the design. Tasks: one estimation script per specification (main, alternate outcome, alternate controls). Verification: tab_main_results.tex exists, coefficients reproducible.

6. Robustness

Canonical checks for the design (via robustness-checks). Tasks: one script per check, one table or column per check. Verification: tab_robustness.tex exists; all checks present; failures discussed.

7. Writing

Paper sections from data to narrative. Tasks: draft each section (Abstract, Introduction, Data, Methods, Results, Discussion, Conclusion), pull tables and figures via \input{} and \includegraphics{}. Writing tasks operate under academic-baseline and must include paper-writing in Skills involved — that skill carries the section formulas, style rules, AI-pattern avoidance, and review rubric. Use journal-guidelines here only when the work is already tied to a specific journal template or formatting requirement. Verification: paper.tex compiles with compile-latex.

8. Submission

Target journal, formatting, checklist. Tasks: invoke journal-selection if not already decided, then invoke journal-guidelines for the chosen journal, adapt the manuscript and submission materials, and run the final compliance check. Journal-facing work without journal-guidelines is invalid. Verification: submission checklist complete.

Task Template

Every task must specify:

Title — imperative, actionable (e.g., "Collect unemployment series from IBGE")
Phase — one of the 8 above
Inputs — files or datasets this task reads
Outputs — files this task produces
Script — path to the script that implements it (e.g., code/01_collect.R)
Verification — command or check to verify the task completed (file exists and is non-empty, script exits 0, pipeline still runs end-to-end)
Skills involved — which superpapers skills are invoked. This field is mandatory routing metadata: include academic-baseline on every task, add the relevant domain skills (e.g., statistical-modeling, tables-and-figures, data-collection), and include journal-guidelines on every journal-facing task
Commit message — exact message to use after the task succeeds

Anti-Patterns

Plan organized by software phases (architecture, backend, frontend) instead of research phases
Omitting the Literature phase — every empirical paper plan must include at least one full-literature-review task routed to literature-search in full mode, producing a curated bibliography before data collection begins
Tasks with vague outputs ("build the analysis", "write the results section")
Tasks without verification criteria
Skipping the manifest update in the collection phase
Hardcoding numeric results in the writing phase
Planning robustness checks before knowing the main result's design
A task that mixes multiple phases
Omitting academic-baseline from a task's Skills involved
Scheduling journal-facing work without journal-guidelines
Placeholders anywhere in the plan — any "fill in later" marker or empty step
Using "similar to Task N" instead of repeating the details — tasks are often read in isolation

Verification Before Completion

Every spec requirement mapped to at least one task
All 8 phases represented, or a phase explicitly excluded with reason
Literature phase includes a task that invokes literature-search in full mode and populates the bibliography
Every task has inputs, outputs, script path, verification, skills, commit message
Every task includes academic-baseline plus the necessary domain skills
Every journal-facing task includes journal-guidelines (or journal-selection followed by journal-guidelines when the outlet is still undecided)
No placeholders in the plan
Dependencies between tasks explicit
Plan saved to docs/superpapers/plans/ in English
Self-review completed
Execution options (execute-plan subagent-driven vs inline) offered to the user