papersmart

Generate or substantially revise full PaperSmart manuscripts from active project materials, including literature evidence, data analysis plans, visualization plans, claim-source mapping, tables, figures, manuscript text, references, and quality checks. Use when the user asks to draft a full paper, write a manuscript, produce Results/Discussion from data, rebuild a major section, integrate literature into a manuscript, or create a journal-ready PaperSmart draft.

Create or revise PaperSmart manuscript outlines, argument maps, article structures, section plans, figure/table plans, and evidence plans from an active project. Use when the user asks for a paper outline, research-paper structure, manuscript plan, argument framework, journal-specific outline, literature-backed outline, or conceptual architecture before full drafting.

Resolve PaperSmart inline AIREF markers by finding suitable scholarly or authoritative evidence, adding citation markers, revising the marked claim when needed, and logging the citation decision. Use when a manuscript contains markers such as *content*AIREF or when the user asks to support marked claims with literature or evidence.

Plan, create, revise, audit, and caption PaperSmart manuscript figures, tables, workflow diagrams, data visualizations, and composite figures using project evidence and journal requirements. Use when the user asks for figure planning, visualization plans, manuscript-ready scientific diagrams, data plots, figure captions, figure QA, image orientation checks, or updates to 03_output/figures and 03_output/supplement/visualization_plan.md.

Apply focused local revisions to an existing PaperSmart manuscript while preserving source integrity, evidence traceability, figure/table numbering, citations, and change logs. Use when the user asks for local edits, reviewer-style fixes, section polishing, targeted restructuring, citation cleanup, caption updates, inline AIGEN/AIPO markers, or specific changes after 03_output/manuscript/paper.md already exists.

Safely update an existing PaperSmart workspace to the current folder and template structure without overwriting project files, shared resources, memory, drafts, references, outputs, revision records, or submission packages. Use when PaperSmart has been upgraded, a workspace is missing newer folders such as writing_samples, a profile needs to be rebuilt, or older projects need non-destructive structure migration.

Initialize a PaperSmart scientific-manuscript workspace or a new PaperSmart project folder in English or Chinese, including the projects/shared directory model, required draft/reference/output/config/log templates, writing_samples, language profile, and companion skills. Use when the user asks to set up PaperSmart, create the base file system, choose English or Chinese workspace mode, scaffold a manuscript project, install dependencies, or prepare a reusable PaperSmart workspace for other users.

Create a new paper-specific project folder inside an existing PaperSmart workspace, using the workspace language profile to scaffold English or Chinese folders, config/draft/reference/output/log directories, writing_samples, starter templates, and active-project memory. Use when the user starts a new manuscript, paper, article, research project, journal submission, or wants a fresh project folder without re-running full PaperSmart initialization.

Prepare PaperSmart journal submission packages from a completed manuscript, including title page, anonymized or main manuscript files, figure captions, tables, declarations, cover letter drafts, metadata templates, submission checklists, and package QA. Use when the user asks to prepare a submission, journal package, cover letter, title page, anonymized manuscript, declarations, figure files, or 03_output/submission outputs.

Translate or localize an existing PaperSmart manuscript into polished Chinese academic prose while preserving scientific meaning, evidence boundaries, citations, figure/table numbering, TODO markers, and declarations. Use when the user asks for a Chinese academic translation, Chinese journal-style version, bilingual preparation, Chinese collaborator version, or 03_output/translation/paper_zh.md.