docrev 0.2.1 → 0.5.0

package/skill/REFERENCE.md

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+# docrev Command Reference
+
+## Document Import/Export
+
+### rev import
+Import a Word document with track changes and comments.
+```bash
+rev import --file manuscript.docx
+rev import -f manuscript.docx --output ./project
+```
+
+### rev build
+Build output documents from markdown sections.
+```bash
+rev build                    # Build PDF and DOCX
+rev build pdf                # PDF only
+rev build docx               # DOCX only
+rev build --toc              # Include table of contents
+```
+
+### rev preview
+Build and open document in default app.
+```bash
+rev preview pdf              # Build and open PDF
+rev preview docx             # Build and open Word
+```
+
+### rev export
+Export project as distributable zip.
+```bash
+rev export                   # Creates project.zip (no node_modules)
+```
+
+### rev backup
+Create timestamped project backup.
+```bash
+rev backup                   # Creates backup-2024-12-29.zip
+rev backup --name v1-draft   # Creates v1-draft.zip
+```
+
+## Comments & Annotations
+
+### rev comments
+List all comments with context.
+```bash
+rev comments methods.md                    # Show comments
+rev comments methods.md --export out.csv   # Export to CSV
+```
+
+### rev reply
+Reply to a specific comment (non-interactive).
+```bash
+rev reply methods.md -n 1 -m "Added clarification"
+rev reply results.md -n 3 -m "Updated figure"
+```
+
+### rev resolve
+Mark a comment as resolved.
+```bash
+rev resolve methods.md -n 1
+rev resolve methods.md -n 1,2,3   # Multiple comments
+```
+
+### rev status
+Show annotation counts for a file.
+```bash
+rev status methods.md
+```
+
+### rev strip
+Remove all annotations from markdown.
+```bash
+rev strip methods.md --output clean.md
+rev strip methods.md --accept          # Accept all changes
+rev strip methods.md --reject          # Reject all changes
+```
+
+## Response Letter
+
+### rev response
+Generate point-by-point response letter from comments.
+```bash
+rev response                 # Generate response letter
+```
+
+## Validation & Checks
+
+### rev check
+Run all pre-submission checks (lint + grammar + citations).
+```bash
+rev check                    # Run all checks
+rev check --fix              # Auto-fix where possible
+```
+
+### rev lint
+Check for common issues.
+```bash
+rev lint                     # Run all checks
+rev lint --fix               # Auto-fix where possible
+```
+Checks: broken cross-references, missing citations, orphaned figures, unresolved comments.
+
+### rev grammar
+Check grammar and style.
+```bash
+rev grammar                  # Check all sections
+rev grammar --rules          # List available rules
+rev grammar --learn word     # Add to custom dictionary
+rev grammar --forget word    # Remove from dictionary
+rev grammar --list           # Show custom dictionary
+rev grammar -s warning       # Filter by severity
+```
+
+### rev spelling
+Check spelling in all sections.
+```bash
+rev spelling                 # Check all sections
+rev spelling --british       # Use British English dictionary
+rev spelling --learn word    # Add to global dictionary (~/.rev-dictionary)
+rev spelling --learn-project word  # Add to project dictionary
+rev spelling --forget word   # Remove from global dictionary
+rev spelling --list          # Show global dictionary
+rev spelling --list-all      # Show global + project dictionaries
+```
+Built-in scientific vocabulary reduces false positives. Possible author names are shown separately for easy review.
+
+### rev validate
+Check against journal requirements.
+```bash
+rev validate --journal nature
+rev validate --list          # List 21 available journals
+```
+
+### rev citations
+Validate citations against bibliography.
+```bash
+rev citations
+```
+
+## DOI Management
+
+### rev doi check
+Validate DOIs in bibliography.
+```bash
+rev doi check references.bib
+rev doi check references.bib --strict   # Fail if articles missing DOIs
+```
+
+### rev doi lookup
+Find missing DOIs by title/author/year.
+```bash
+rev doi lookup references.bib
+rev doi lookup references.bib --confidence high
+```
+
+### rev doi fetch
+Get BibTeX from a DOI.
+```bash
+rev doi fetch 10.1234/example
+```
+
+### rev doi add
+Add citation to .bib file from DOI.
+```bash
+rev doi add 10.1234/example
+rev doi add 10.1234/example --file references.bib
+```
+
+## Content Analysis
+
+### rev word-count
+Show word counts per section.
+```bash
+rev word-count               # Per-section counts
+rev word-count --limit 5000  # Warn if over limit
+rev word-count -j nature     # Use journal word limit
+```
+
+### rev stats
+Project dashboard showing overview.
+```bash
+rev stats                    # Words, figures, citations, comments
+```
+
+### rev search
+Search across all section files.
+```bash
+rev search "climate change"
+rev search -i "method"       # Case-insensitive
+```
+
+### rev figures
+List figures with reference counts.
+```bash
+rev figures methods.md
+```
+
+### rev equations
+Work with LaTeX equations.
+```bash
+rev equations list           # List all equations
+rev equations from-word manuscript.docx  # Extract from Word
+```
+
+## Direct DOCX Editing
+
+### rev annotate
+Add comments directly to Word document.
+```bash
+rev annotate paper.docx -m "Comment" -s "text to find"
+```
+
+### rev apply
+Apply MD annotations as Word track changes.
+```bash
+rev apply paper.md output.docx
+```
+
+### rev comment
+Interactive comment mode for Word documents.
+```bash
+rev comment paper.docx
+```
+
+## Project Management
+
+### rev init
+Initialize a new paper project.
+```bash
+rev init my-paper
+rev init my-paper --template apa
+```
+
+### rev sections
+List and manage section files.
+```bash
+rev sections                 # List all sections
+```
+
+### rev clean
+Remove generated files.
+```bash
+rev clean                    # Remove paper.md, PDFs, DOCXs
+rev clean --dry-run          # Show what would be deleted
+rev clean --all              # Also remove backups and exports
+```
+
+### rev open
+Open project folder or file.
+```bash
+rev open                     # Open project folder
+rev open paper.pdf           # Open specific file
+```
+
+### rev watch
+Auto-rebuild on file changes.
+```bash
+rev watch                    # Watch and rebuild
+rev watch pdf                # Only rebuild PDF
+rev watch --no-open          # Don't open after build
+```
+
+## Configuration
+
+### rev config
+Configure user settings.
+```bash
+rev config user "Your Name"  # Set author name for replies
+rev config                   # Show current config
+```
+
+## Shell Completions
+
+### rev completions
+Output shell completions.
+```bash
+eval "$(rev completions bash)"  # Bash
+eval "$(rev completions zsh)"   # Zsh
+```

package/skill/SKILL.md

@@ -0,0 +1,137 @@
+---
+name: docrev
+description: "Academic paper revision workflow tool (CLI: `rev`). Use when working with Word documents containing reviewer comments, importing track changes to markdown, replying to reviewer comments, building PDF/DOCX outputs, generating response letters, validating citations/DOIs, or any academic paper revision task."
+---
+
+# docrev - Academic Paper Revision Tool
+
+`rev` is a CLI tool for academic paper workflows with Word ↔ Markdown round-trips.
+
+## Core Workflow
+
+### 1. Import reviewed Word document
+
+```bash
+rev import --file manuscript-reviewed.docx
+```
+
+This extracts track changes and comments as CriticMarkup annotations in markdown files.
+
+### 2. View and address comments
+
+```bash
+rev comments methods.md              # List all comments with context
+rev status methods.md                # Show annotation counts
+```
+
+### 3. Reply to reviewer comments
+
+**Always use the non-interactive reply mode:**
+
+```bash
+rev reply methods.md -n 1 -m "Added clarification about sampling methodology"
+rev reply results.md -n 3 -m "Updated figure to include 95% CI"
+```
+
+Replies appear as: `{>>Reviewer: Original<<} {>>User: Reply<<}`
+
+### 4. Resolve addressed comments
+
+```bash
+rev resolve methods.md -n 1          # Mark comment #1 as resolved
+```
+
+### 5. Build output documents
+
+```bash
+rev build                            # Build both PDF and DOCX
+rev build docx                       # Word only
+rev build pdf                        # PDF only
+rev build --toc                      # Include table of contents
+```
+
+### 6. Generate response letter
+
+```bash
+rev response                         # Generate point-by-point response letter
+```
+
+## Annotation Syntax (CriticMarkup)
+
+- `{++inserted text++}` - Additions
+- `{--deleted text--}` - Deletions
+- `{~~old~>new~~}` - Substitutions
+- `{>>Author: comment<<}` - Comments
+- `{>>Author: comment [RESOLVED]<<}` - Resolved comment
+
+## Quick Commands
+
+| Task | Command |
+|------|---------|
+| Word count per section | `rev word-count` |
+| Word count with limit | `rev word-count --limit 5000` |
+| Project dashboard | `rev stats` |
+| Search all sections | `rev search "query"` |
+| Pre-submission check | `rev check` |
+| Validate citations | `rev citations` |
+| Check grammar/style | `rev grammar` |
+| Check spelling | `rev spelling` |
+| Open PDF preview | `rev preview pdf` |
+| Auto-rebuild on changes | `rev watch` |
+
+## DOI Management
+
+```bash
+rev doi check references.bib         # Validate DOIs
+rev doi lookup references.bib        # Find missing DOIs
+rev doi add 10.1234/example          # Add citation from DOI
+```
+
+## Validation
+
+```bash
+rev validate --journal nature        # Check journal requirements
+rev validate --list                  # List 21 available journal profiles
+rev lint                             # Check broken refs, missing citations
+```
+
+## Cross-References
+
+Use in markdown files:
+- `@fig:label` - Figure reference (becomes "Figure 1" in Word)
+- `@tbl:label` - Table reference
+- `@eq:label` - Equation reference
+- `{#fig:label}` - Anchor for figures
+
+## Template Variables
+
+Available in section files (processed during build):
+- `{{date}}` - Current date (YYYY-MM-DD)
+- `{{date:MMMM D, YYYY}}` - Custom format
+- `{{title}}` - Document title
+- `{{author}}` - First author
+- `{{word_count}}` - Total word count
+
+## Project Structure
+
+```
+my-paper/
+├── rev.yaml           # Project config
+├── introduction.md    # Section files with annotations
+├── methods.md
+├── results.md
+├── discussion.md
+├── references.bib     # Bibliography
+├── figures/           # Images
+└── paper.docx         # Built output
+```
+
+## When Helping Users
+
+1. **Import phase**: Run `rev import` to get track changes as markdown
+2. **Review phase**: Use `rev comments` to see all comments, then `rev reply` to respond
+3. **Build phase**: Run `rev build docx` to generate the updated Word document
+4. **Validation phase**: Run `rev check` before submission (lint + grammar + citations)
+5. **Response letter**: Use `rev response` to generate point-by-point responses
+
+For complete command reference, see [REFERENCE.md](REFERENCE.md).