PaperHarbor

A structured environment for scholarly manuscript development, emphasizing evidence-grounded revision and publication-ready LaTeX output.
This repository intentionally avoids runtime automation and focuses on:

• structured writing assets (tex, figures, results, notes),
• reproducible manuscript organization,
• modular writing skills for literature, method, and experiments support.

Highlights

• No hidden pipeline: no compile/run/patch CLI workflow.
• Skill-driven editing: open a specific Skill only when needed.
• Publication-oriented layout: one paper folder per submission.
• Portable build: standard pdflatex + bibtex.

Repository Layout

.
├── AGENT.md                         # staged writing workflow (A→F)
├── HANDBOOK.md                      # directory conventions and asset placement
├── guide/README.md                  # quick navigation
├── skills/                          # task-specific Skill packages
├── schemas/                         # optional JSON schemas used by Skills
├── papers/
│   ├── _template/                   # starter skeleton for new papers
│   └── my-paper-2026/               # active writing workspace
├── docs/                            # status/contracts/quality notes
└── manuscript_writing_runtime_design.md  # archived historical design doc

Quick Start

1. Copy papers/_template/ to a new paper id (or continue in papers/my-paper-2026/).
2. Edit manuscript in assets/tex/main.tex.
3. Put figures in assets/figures/, result tables in assets/results/.
4. Use AGENT.md to run staged Agent assistance.

Build PDF

From your paper's assets/tex/ directory:

pdflatex -interaction=nonstopmode main.tex
bibtex main
pdflatex -interaction=nonstopmode main.tex
pdflatex -interaction=nonstopmode main.tex

Skill-Oriented Workflow

Use the staged flow in AGENT.md:

• A: manuscript structure and bibliography hygiene
• B: related work scouting/review
• C: method formula analysis/review
• D: experiment observation analysis/review
• E: orchestration/checkpointing
• F: final drafting and polishing in main.tex

figure-import-curator is optional and should only be invoked when explicitly requested.

Version Control Notes

• .gitignore is configured for LaTeX intermediates, OS artifacts, and local editor caches.
• Keep source assets versioned (.tex, .bib, figures, CSV tables, notes).
• Avoid committing generated transient files (.aux, .log, .bbl, etc.).

Scope and Non-Goals

• This repository is a writing system, not a training/inference framework.
• Acceptance-quality results still depend on research novelty and experimental rigor.
• Historical runtime concepts are preserved only as archival notes in manuscript_writing_runtime_design.md.

Entry Points

• Workflow: AGENT.md
• Asset conventions: HANDBOOK.md
• Active paper workspace: papers/my-paper-2026/README.md