superpaper-init

name: superpaper-init description: Use when starting a new dissertation project or adopting an existing repo for dissertation work

Init

When to Use

User says "start a new paper", "start a new dissertation project", "new paper project"
User wants to organize an existing repo for dissertation writing
No meta/ directory exists in the current project
User says "init", "initialize this project", or "set up superpaper"

Procedure

Determine which mode applies. If the current directory has substantial existing content (markdown files, code, data), offer init adopt. If it is empty or has only a README, proceed with init new.

Ask the user to confirm the mode if unclear.

Mode 1: New Project (`init new`)

Interactive setup — ask these questions one at a time before creating any files:

Paper language? (zh / en) — default: zh
Paper title?
Citation style? (GB/T 7714 / APA / Chicago / IEEE / custom) — default: GB/T 7714
Chapter structure? Offer templates:
- Social science: Introduction, Literature Review, Theoretical Framework, Research Design, Findings, Discussion, Conclusion
- STEM: Introduction, Literature Review, Methodology, Results, Discussion, Conclusion
- Custom: user defines their own chapter names
University? (for dissertation formatting and context) — optional, user can skip

Once answers are collected, scaffold the full project structure:

<project>/
  CLAUDE.md
  AGENTS.md
  GEMINI.md

  meta/
    memory.md          # Initialize with project creation entry
    progress.md        # All chapters marked as [NOT STARTED]
    milestones.md      # Empty template
    plan.md            # Empty template
    style/
    tasks/

  writings/
    ch01-<name>/
      outline.md
      resources.md
      draft.md
      status.md
      assets/
      reviews/
    ch02-<name>/
      ...

  references/
    literature/
    results/
    docs/

  .gitignore

File generation steps:

Create all directories. Use ch01-<slug>, ch02-<slug>, ... based on chapter names provided.
Generate meta/memory.md:

# Memory

## Current Focus
Project just initialized: <title>

## Recent Decisions
- <date>: Project created with <citation style> citation style, language: <language>

## Open Questions

## Key Insights

## Next Session
- Run `checkin` to begin your first session
- Consider running `brainstorm` to explore research directions

Generate meta/progress.md:

# Progress

| Chapter | Status | Notes |
|---------|--------|-------|
| ch01 — <name> | [NOT STARTED] | |
| ch02 — <name> | [NOT STARTED] | |
...

Generate meta/milestones.md:

# Milestones

| Milestone | Target Date | Status |
|-----------|-------------|--------|
| Topic finalized | | [ ] |
| Literature review complete | | [ ] |
| Outline approved | | [ ] |
| First draft complete | | [ ] |
| Revisions complete | | [ ] |
| Submission | | [ ] |

Generate meta/plan.md as an empty template with headers: # Plan, ## Timeline, ## Weekly Routine.
Generate writings/ch0N-<name>/status.md for each chapter:

# <Chapter Name> Status

## Sections
(to be filled during outline)

## Blockers

## Last Updated
<date> by init

6b. Generate writings/ch0N-<name>/outline.md for each chapter as an empty placeholder:

# Chapter N: <Chapter Name>

## Outline

*To be drafted. Run `superpaper-outline` to plan this chapter.*

6c. Generate writings/ch0N-<name>/draft.md for each chapter as an empty placeholder:

# Chapter N: <Chapter Name>

## Draft

*Not yet started. Complete the outline first, then run `superpaper-draft`.*

6d. Generate writings/ch0N-<name>/resources.md for each chapter as an empty placeholder:

# Chapter N: <Chapter Name> — Resources

## Literature

*No references yet. Run `superpaper-ingest` to add literature.*

## Results

*No analysis results yet.*

Generate CLAUDE.md with full project settings (see template below).
Generate AGENTS.md referencing the same project settings and skill mapping as CLAUDE.md.
Generate GEMINI.md with tool mapping reference (activate_skill maps to Skill tool in Claude Code).
Generate .gitignore (see template below).
Run:

# If git not already initialized, run git init first
git init   # safe to run even if already initialized (no-op)
git add .
git commit -m "init: <title>"

Note: Check if .git/ already exists. If so, skip git init to avoid confusing output — run git add . && git commit -m "init: <title>" directly.

Print next steps:

Project scaffolded. Run checkin to start your first session, or brainstorm to explore research directions.

Mode 2: Adopt Existing Repo (`init adopt`)

Key principle: adopt mode never moves or deletes existing files without explicit confirmation from the user. This is non-negotiable — NEVER alter or remove existing content without asking.

For repos with existing content:

Paper language? (zh / en)
Paper title?
Citation style? (GB/T 7714 / APA / Chicago / IEEE / custom)
Scan the repo for content patterns:
- Markdown files → potential chapter drafts
- PDF files → potential literature copies
- Code/data directories → potential results/analysis
- Zotero exports (CSL-JSON, BibTeX .bib files) → literature references
- Existing directory structure
Present proposed mapping to the user. Example:

Found content:
  chapters/intro.md  →  writings/ch01-introduction/draft.md (symlink/record in CLAUDE.md)
  chapters/lit.md    →  writings/ch02-literature/draft.md
  data/              →  references/results/
  refs.bib           →  references/literature/ (after ingest)

No files will be moved. Mapping recorded in CLAUDE.md.
Confirm? (yes / adjust)

After user confirmation, create the meta/ layer on top:
- meta/memory.md — initial entry describing the adoption and what was found
- meta/progress.md — chapters with existing drafts marked as [IN PROGRESS], others as [NOT STARTED]
- Per-chapter status.md for each identified chapter
If the existing structure uses different directory names (e.g., chapters/ instead of writings/), record the mapping in CLAUDE.md under a ## Directory Mapping section. Do not rename directories.
Generate CLAUDE.md / AGENTS.md / GEMINI.md.
Commit: "init: adopt existing repo — <title>"

CLAUDE.md Template

Generate this in the user's project root:

# <Paper Title>

## Project Settings
- Language: <language>
- Citation style: <citation style>
- University: <from question 5, or blank if user skipped>

## Skills
This project uses superpaper.
Before any task, check for a matching skill.

### Project Manager
- Session start → superpaper-checkin
- New materials → superpaper-ingest
- End of session → superpaper-memory-update

### Research Facilitator
- Topic exploration → superpaper-brainstorm
- Literature gaps → superpaper-research
- Data questions → superpaper-data-explore / superpaper-analysis

### Writing Assistant
- Chapter planning → superpaper-outline
- Writing → superpaper-draft
- Reviewing → superpaper-review

### Quality Assurance
- Audit → superpaper-lint
- Submission prep → superpaper-export

## Context Loading
1. Read meta/memory.md — recent history and decisions
2. Read meta/progress.md — overall state
3. Read relevant writings/<ch>/status.md — chapter details
4. Read relevant references/<key>/summary.md — don't re-read originals

## Writing Principles
- Mark uncertainty: [TODO], [CITE], [DATA]. Never fabricate.
- Always structurally complete. Missing sections have placeholders.
- Respect human edits. Never overwrite without asking.
- Follow meta/style/style-guide.md — extracted from sample paragraphs/chapters you provide.
- Shorter is better.
- Task files in `meta/tasks/` should have a status header: `status: pending | in-progress | done`. Stale done tasks can be archived to `meta/tasks/archive/`.

## Boundaries
- Do not fabricate data, results, or citations
- Do not mark chapters as finalized (human only)
- Do not make major structural changes without asking
- Do not delete human content without permission
- For deep research: generate prompts, don't pretend to search
- For coding/analysis: generate specs, don't write code

.gitignore Template

# PDFs (markdown-first — PDFs are local reference copies)
*.pdf

# Data files
*.csv
*.xlsx
*.dta
*.sav
*.rds

# Large binary files
*.zip
*.tar.gz

# Assets (figures regenerated from code)
writings/*/assets/*
!writings/*/assets/.gitkeep

# OS
.DS_Store
Thumbs.db

# Editor
.idea/
.vscode/
*.swp

# Exported drafts (regenerate with export skill)
export/

Inputs

User's answers to interactive prompts (language, title, citation style, chapter structure)
For adopt mode: existing repo content

Outputs

Full project directory structure
meta/memory.md, meta/progress.md, meta/milestones.md, meta/plan.md
Per-chapter writings/ch0N-<name>/ directories with placeholder files
references/literature/, references/results/, references/docs/
CLAUDE.md, AGENTS.md, GEMINI.md with project settings and skill mapping
.gitignore
Initial git commit

Notes

Chapter directories: ch01-<slug>, ch02-<slug>, etc. Slugify names (lowercase, hyphens).
Generated files should match the project language setting (use Chinese headings for zh projects).
The generated CLAUDE.md is what any agent reads when entering the dissertation project.
For adopt mode: if no title is found, ask before proceeding.
Suggest checkin as the very next skill to run after init completes.