docrev 0.6.2 → 0.6.3

package/README.md

@@ -1,11 +1,10 @@
 # docrev
 
 [![npm](https://img.shields.io/npm/v/docrev)](https://www.npmjs.com/package/docrev)
-[![CI](https://github.com/gcol33/docrev/actions/workflows/ci.yml/badge.svg)](https://github.com/gcol33/docrev/actions/workflows/ci.yml)
 [![Node.js](https://img.shields.io/node/v/docrev)](https://nodejs.org/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
-CLI tool for Word ↔ Markdown round-trips. Handle reviewer feedback on academic papers: import track changes, review interactively, manage comments, validate DOIs, and build to PDF/DOCX/LaTeX.
+CLI tool for academic paper workflows with Word ↔ Markdown round-trips. Handle reviewer feedback, manage comments, validate DOIs, and build to PDF/DOCX/LaTeX.
 
 ## Install
 
@@ -13,411 +12,107 @@ CLI tool for Word ↔ Markdown round-trips. Handle reviewer feedback on academic
 npm install -g docrev
 ```
 
-The `rev` command is now available globally.
-
-### Prerequisites
-
-- **Node.js 18+** - [Download](https://nodejs.org/)
-- **Pandoc** - For building PDF/DOCX ([pandoc.org](https://pandoc.org/installing.html))
-- **pandoc-crossref** - For figure/table refs (optional, [install](https://github.com/lierdakil/pandoc-crossref/releases))
+**Prerequisites:** [Pandoc](https://pandoc.org/installing.html) and optionally [pandoc-crossref](https://github.com/lierdakil/pandoc-crossref)
 
 ```bash
 # macOS
 brew install pandoc pandoc-crossref
 
-# Ubuntu/Debian
-sudo apt install pandoc
-
-# Windows
-winget install JohnMacFarlane.Pandoc
-```
-
-Verify installation:
-```bash
+# Verify
 rev --version
-rev install    # Check for missing dependencies
-```
-
-### Shell Completions (Optional)
-
-Enable tab completion for `rev` commands:
-
-```bash
-# Bash - add to ~/.bashrc
-eval "$(rev completions bash)"
-
-# Zsh - add to ~/.zshrc
-eval "$(rev completions zsh)"
+rev install
 ```
 
-## Features
-
-- **Integrated build system** - Combine sections → paper.md → PDF, DOCX, or LaTeX
-- **Import from Word** - Diff Word docs against your Markdown, generating CriticMarkup annotations
-- **Section-aware import** - Import directly to modular section files (intro.md, methods.md, etc.)
-- **Interactive review** - Accept/reject track changes with a TUI
-- **Comment management** - List, filter, resolve, and reply to reviewer comments
-- **Response letter generation** - Auto-generate point-by-point response from comments
-- **DOI validation** - Check and find DOIs via Crossref/DataCite APIs
-- **Cross-reference conversion** - Auto-convert "Figures 1-3" to `@fig:label` syntax (handles complex patterns)
-- **Equation extraction** - Extract LaTeX equations from Word documents (OMML → LaTeX)
-- **Citation validation** - Check citations against bibliography
-
 ## Quick Start
 
-### Start from Word Document
-
 ```bash
-# Import existing Word doc → creates section files + rev.yaml
-rev import manuscript.docx
-
-# Import to specific directory
-rev import manuscript.docx -o my-paper/
-
-# Preview without creating files
-rev import manuscript.docx --dry-run
-```
-
-### New Project from Template
-
-```bash
-# Create a new paper project
+# Create new project
 rev new my-paper
 
-# or with a specific template
-rev new my-thesis --template thesis
-
-# List available templates
-rev new --list
-```
-
-### Build Workflow
-
-```bash
-cd my-paper
-
-# Edit your sections
-# introduction.md, methods.md, results.md, discussion.md
+# Or import from Word
+rev import manuscript.docx
 
-# Build PDF and Word
-rev build
+# Edit sections: introduction.md, methods.md, results.md, discussion.md
 
-# Build specific format
+# Build outputs
 rev build pdf
 rev build docx
-rev build tex
-rev build all    # PDF + DOCX + TEX
+rev build --dual    # Clean + comments DOCX with threaded comments
 ```
 
-### Review Workflow
+## Reviewer Workflow
 
 ```bash
-# Import reviewer's Word doc to section files
+# Import reviewed Word doc to section files
 rev sections reviewed.docx
 
 # Review track changes interactively
 rev review methods.md
 
-# See remaining comments
+# See and reply to comments
 rev comments methods.md
+rev reply methods.md -n 1 -m "Added clarification"
 
 # Rebuild
-rev build docx
+rev build docx --dual
 ```
 
-## Commands
-
-### Build & Create
-
-| Command | Description |
-|---------|-------------|
-| `rev build [formats...]` | Build PDF/DOCX/TEX from sections |
-| `rev build --toc` | Build with table of contents |
-| `rev build --show-changes` | Export DOCX with visible track changes |
-| `rev new <name>` | Create new project from template |
-| `rev new --list` | List available templates |
-| `rev install` | Check/install dependencies (pandoc-crossref) |
+## Key Features
 
-### Import & Export
+- **Build system** - Sections → paper.md → PDF, DOCX, LaTeX
+- **Word import** - Extracts text, comments, equations (OMML → LaTeX), and images
+- **Interactive review** - Accept/reject track changes with TUI
+- **Comment threading** - Guy→Gilles reply pairs become threaded Word comments
+- **Cross-references** - `@fig:label` → "Figure 1" (auto-converted from Word)
+- **DOI validation** - Check and lookup DOIs via Crossref/DataCite
+- **Journal validation** - Check against 21 journal requirement profiles
 
-| Command | Description |
-|---------|-------------|
-| `rev import <docx>` | Bootstrap project from Word (creates sections + rev.yaml) |
-| `rev import <docx> <md>` | Import changes by diffing Word against your MD |
-| `rev sections <docx>` | Import Word doc to existing section files |
-| `rev extract <docx>` | Extract plain text from Word |
-
-### Review & Edit
-
-| Command | Description |
-|---------|-------------|
-| `rev review <file>` | Interactive accept/reject TUI for track changes |
-| `rev status <file>` | Show annotation counts |
-| `rev comments <file>` | List all comments with context |
-| `rev comments <file> --export comments.csv` | Export comments to CSV |
-| `rev resolve <file> -n 1` | Mark comment #1 as resolved |
-| `rev strip <file>` | Output clean Markdown (annotations applied) |
-
-### Cross-References
-
-| Command | Description |
-|---------|-------------|
-| `rev refs [file]` | Show figure/table registry and reference status |
-| `rev migrate <file>` | Convert hardcoded refs (Fig. 1) to dynamic (@fig:label) |
-
-### Comments & Replies
-
-| Command | Description |
-|---------|-------------|
-| `rev config user "Name"` | Set your name for replies |
-| `rev reply <file>` | Interactive reply to reviewer comments |
-| `rev reply <file> -n 1 -m "text"` | Reply to specific comment (non-interactive) |
-
-### Bibliography & DOIs
-
-| Command | Description |
-|---------|-------------|
-| `rev doi check [file.bib]` | Validate DOIs in bibliography (Crossref + DataCite) |
-| `rev doi lookup [file.bib]` | Search for missing DOIs by title/author/year |
-| `rev doi fetch <doi>` | Fetch BibTeX entry from DOI |
-| `rev doi add <doi>` | Fetch and add DOI entry to bibliography |
-
-### Validation & Analysis
-
-| Command | Description |
-|---------|-------------|
-| `rev citations [file.bib]` | Validate citations against bibliography |
-| `rev figures [file]` | List figures/tables with reference counts |
-| `rev equations list` | List all equations in section files |
-| `rev equations from-word <docx>` | Extract equations from Word to LaTeX |
-| `rev response [files]` | Generate response letter from comments |
-| `rev anonymize <file>` | Prepare document for blind review |
-| `rev validate --journal <name>` | Check manuscript against journal requirements |
-| `rev validate --list` | List available journal profiles |
-
-### Multi-Reviewer & Git
-
-| Command | Description |
-|---------|-------------|
-| `rev merge <md> <docx...>` | Merge feedback from multiple Word documents |
-| `rev diff [ref]` | Compare sections against git history |
-| `rev history [file]` | Show revision history for sections |
-
-### Configuration
-
-| Command | Description |
-|---------|-------------|
-| `rev init` | Generate sections.yaml from existing .md files |
-| `rev split <file>` | Split annotated paper.md back to section files |
-| `rev help [topic]` | Show help (topics: workflow, syntax, commands) |
-
-### Convenience Commands
-
-| Command | Description |
-|---------|-------------|
-| `rev word-count` | Show word counts per section |
-| `rev word-count -j <journal>` | Warn if over journal word limit |
-| `rev stats` | Project dashboard (words, figures, citations) |
-| `rev search <query>` | Search across all section files |
-| `rev backup` | Create timestamped backup zip |
-| `rev export` | Export project as distributable zip |
-| `rev preview <format>` | Build and open document |
-| `rev watch [format]` | Auto-rebuild on file changes |
-| `rev lint` | Check for broken refs, missing citations |
-
-### Grammar & Style
-
-| Command | Description |
-|---------|-------------|
-| `rev grammar` | Check grammar/style issues |
-| `rev grammar --rules` | List available grammar rules |
-| `rev grammar --learn <word>` | Add word to custom dictionary |
-| `rev grammar --list` | Show custom dictionary |
-
-### Spelling
+## Commands
 
 | Command | Description |
 |---------|-------------|
-| `rev spelling` | Check spelling in all sections |
-| `rev spelling --british` | Use British English dictionary |
-| `rev spelling --learn <word>` | Add word to global dictionary |
-| `rev spelling --learn-project <word>` | Add word to project dictionary |
-| `rev spelling --list` | Show global dictionary |
-| `rev spelling --list-all` | Show global + project dictionaries |
+| `rev build [pdf\|docx\|tex]` | Build outputs from sections |
+| `rev build --dual` | Clean + comments DOCX |
+| `rev import <docx>` | Bootstrap project from Word |
+| `rev sections <docx>` | Import to existing section files |
+| `rev review <file>` | Interactive accept/reject TUI |
+| `rev comments <file>` | List comments with context |
+| `rev reply <file> -n N -m "text"` | Reply to comment |
+| `rev doi check [file.bib]` | Validate DOIs |
+| `rev doi lookup [file.bib]` | Find missing DOIs |
+| `rev validate -j <journal>` | Check journal requirements |
+
+See [docs/commands.md](docs/commands.md) for full command reference.
 
-### Direct DOCX Editing
+## Annotation Syntax (CriticMarkup)
 
-| Command | Description |
-|---------|-------------|
-| `rev annotate <docx>` | Add comments to Word document |
-| `rev apply <md> <docx>` | Apply annotations as track changes |
-| `rev comment <docx>` | Interactive comment mode |
+```markdown
+{++inserted text++}      # Insertions
+{--deleted text--}       # Deletions
+{~~old~>new~~}           # Substitutions
+{>>Author: comment<<}    # Comments
+```
 
 ## Project Structure
 
-A typical rev project:
-
 ```
 my-paper/
-├── rev.yaml           # Project config (title, authors, build settings)
+├── rev.yaml           # Config (title, authors, build settings)
 ├── introduction.md    # Section files
 ├── methods.md
 ├── results.md
 ├── discussion.md
 ├── references.bib     # Bibliography
 ├── figures/           # Images
-├── paper.md           # Combined output (generated)
-├── my-paper.pdf       # PDF output (generated)
-└── my-paper.docx      # Word output (generated)
-```
-
-## Configuration (rev.yaml)
-
-```yaml
-title: "Your Paper Title"
-authors:
-  - name: First Author
-    affiliation: Institution
-    email: author@example.com
-
-sections:
-  - introduction.md
-  - methods.md
-  - results.md
-  - discussion.md
-
-bibliography: references.bib
-csl: nature.csl           # Optional citation style
-
-crossref:
-  figureTitle: Figure
-  tableTitle: Table
-  figPrefix: [Fig., Figs.]
-  tblPrefix: [Table, Tables]
-
-pdf:
-  documentclass: article
-  fontsize: 12pt
-  geometry: margin=1in
-  linestretch: 1.5
-  toc: false                 # Table of contents
-
-docx:
-  reference: template.docx   # Optional reference doc
-  keepComments: true
-  toc: false                 # Table of contents
-```
-
-## Annotation Syntax (CriticMarkup)
-
-```markdown
-{++inserted text++}      # Insertions
-{--deleted text--}       # Deletions
-{~~old~>new~~}           # Substitutions
-{>>Author: comment<<}    # Comments
-```
-
-## Template Variables
-
-Use template variables in section files (processed during build):
-
-```markdown
-Last updated: {{date}}
-Version: {{version}}
-Word count: {{word_count}}
-```
-
-| Variable | Description |
-|----------|-------------|
-| `{{date}}` | Current date (YYYY-MM-DD) |
-| `{{date:MMMM D, YYYY}}` | Custom format (December 29, 2025) |
-| `{{year}}` | Current year |
-| `{{version}}` | Version from rev.yaml |
-| `{{title}}` | Document title |
-| `{{author}}` | First author name |
-| `{{authors}}` | All authors (comma-separated) |
-| `{{word_count}}` | Total word count |
-
-## Comment Replies
-
-Reply to reviewer comments with your name:
-
-```bash
-# Set your name (once)
-rev config user "Gilles Colling"
-
-# Interactive: go through each comment
-rev reply methods.md
-
-# Non-interactive: reply to specific comment
-rev reply methods.md -n 1 -m "Done, added clarification"
-```
-
-Creates a conversation thread:
-```markdown
-{>>Reviewer: Please clarify this<<} {>>Gilles Colling: Added in next paragraph<<}
-```
-
-Claude can also reply programmatically using the non-interactive mode.
-
-## Cross-Reference System
-
-Use dynamic references in your source:
-
-```markdown
-![Caption](figures/img.png){#fig:heatmap}
-
-See @fig:heatmap for the results.
+└── paper.docx         # Generated output
 ```
 
-When importing from Word, hardcoded refs are auto-converted:
-- `Figure 1` → `@fig:heatmap`
-- `Fig. 2a` → `@fig:model`
-- `Figs. 1-3` → `@fig:heatmap; @fig:model; @fig:hierarchy`
-- `Figures 1, 2, and 3` → `@fig:one; @fig:two; @fig:three`
-- `Fig. 1a-c` → `@fig:one` (expands letter suffixes)
-- `Figs. 1a-3b` → all panels from 1a to 3b
-
-## Build Outputs
-
-| Format | Annotations | Cross-refs |
-|--------|-------------|------------|
-| PDF | Stripped (clean) | `@fig:label` → "Figure 1" |
-| DOCX | Comments kept | `@fig:label` → "Figure 1" |
-| TEX | Stripped (clean) | LaTeX labels |
-
-## DOI Management
-
-Check and find DOIs for your bibliography:
-
-```bash
-# Validate all DOIs in references.bib
-rev doi check references.bib
-
-# Look up missing DOIs automatically
-rev doi lookup references.bib --confidence medium
-
-# Fetch BibTeX from a DOI
-rev doi fetch 10.1038/nature12373
-
-# Add a citation by DOI
-rev doi add 10.1038/nature12373
-```
-
-**Features:**
-- Validates DOIs via Crossref API (+ DataCite for Zenodo/Figshare)
-- Smart lookup using title, author, year, and journal matching
-- Filters out supplement/figure DOIs and F1000 reviews
-- Confidence levels: `high`, `medium`, `low` (use `--confidence low` to see all matches)
-- Skip entries with `nodoi = {true}` or `% no-doi` comment
-
-## Dependencies
+## Documentation
 
-- Node.js 18+
-- [Pandoc](https://pandoc.org/) - Document conversion
-- [pandoc-crossref](https://github.com/lierdakil/pandoc-crossref) - Cross-references (optional but recommended)
-- [mammoth](https://github.com/mwilliamson/mammoth.js) - Word document parsing
-- [diff](https://github.com/kpdecker/jsdiff) - Text diffing
+- [Commands Reference](docs/commands.md) - All commands with examples
+- [Configuration](docs/configuration.md) - rev.yaml options
+- [Workflow Guide](docs/workflow.md) - Step-by-step reviewer workflow
+- [API Reference](docs/api.md) - Library usage
 
 ## License
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "docrev",
-  "version": "0.6.2",
+  "version": "0.6.3",
   "description": "Academic paper revision workflow: Word ↔ Markdown round-trips, DOI validation, reviewer comments",
   "type": "module",
   "types": "types/index.d.ts",