Workflow Quick Reference — Manuscript Submission Formatting Agent

Workflow Quick Reference — Manuscript Submission Formatting Agent

**Model:** Contractor (you direct, Claude orchestrates)

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The Loop

Your instruction
    ↓
[PLAN] (if multi-file or unclear) → Show plan → Your approval
    ↓
[EXECUTE] Ingest → Analyze → Reformat → Export → Compliance check → Report
    ↓
[REPORT] Summary + output files + required author actions
    ↓
Repeat

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Core Workflow (Start Here)

# Step 1: Parse journal guidelines (one-time per journal)
/parse-guidelines [journal-name] [URL]

# Step 2: Format the manuscript
/format-manuscript manuscripts/paper.docx [journal-name]

# Step 3: Review draft sections, then validate
/validate-compliance outputs/[journal]/manuscript_formatted.md [journal-name]

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I Ask You When

• Design forks: "Manuscript has two Results sections — merge or keep?"
• Content ambiguity: "Cannot determine which paragraph maps to 'Background' — clarify?"
• Scope question: "Also proofread while formatting, or just format?"
• Missing data: "Cannot auto-draft Data Availability — do you have a repository URL?"

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I Just Execute When

• Formatting is rules-based (section reorder, heading rename, heading case)
• Ingest / export commands
• Compliance checking (mechanical against guidelines YAML)
• Auto-drafting from existing content (always marked DRAFT)
• Proofreading (report only, no edits)

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Quality Gates (No Exceptions)

Score	Action
>= 80	Ready to commit / deliver
< 80	Fix blocking compliance issues first

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Non-Negotiables

• Never alter scientific content — only formatting, structure, headings
• Draft markers always used — on all auto-generated content
• manuscripts/ is read-only — always work in outputs/
• Both .md and .docx delivered — never just one format

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Preferences

**Reporting:** Concise bullet summary + full compliance checklist in separate file **Draft sections:** Always mark, never silently insert **Session logs:** Always (post-plan, incremental, end-of-session) **Word count:** Flag WARN but never cut content automatically

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Exploration Mode

For testing or experimenting with new journals, use the **Fast-Track** workflow:

• Work in explorations/ folder
• 60/100 quality threshold (vs. 80/100 for production)
• No plan needed — just a value check
• See .claude/rules/exploration-fast-track.md

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Key File Locations

What	Where
Input manuscripts	manuscripts/ (read-only)
Journal guidelines	guidelines/[journal].yml
Working copy	outputs/[journal]/working.md
Formatted output	outputs/[journal]/manuscript_formatted.md/.docx
Compliance report	outputs/[journal]/compliance_checklist.md
Formatting report	outputs/[journal]/formatting_report.md
Reference template	templates/reference.docx
Guidelines schema	`templates/jo