docrev 0.2.0

package/CLAUDE.md

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+# Claude Instructions for rev
+
+This is `rev`, a CLI tool for academic paper workflows with Word ↔ Markdown round-trips.
+
+## Key Commands for Claude
+
+### Replying to Comments
+When helping the user address reviewer comments, use the non-interactive reply mode:
+
+```bash
+# Reply to a specific comment by number
+rev reply <file> -n <number> -m "Your response"
+
+# Example
+rev reply methods.md -n 1 -m "Added clarification about sampling methodology in paragraph 2"
+```
+
+The user's name is already configured via `rev config user`. Replies appear as:
+```markdown
+{>>Reviewer: Original comment<<} {>>User Name: Your reply<<}
+```
+
+### Viewing Comments
+```bash
+rev comments <file>       # List all comments with context
+rev status <file>         # Show annotation counts
+```
+
+### Building Documents
+```bash
+rev build                 # Build PDF and DOCX
+rev build pdf             # PDF only
+rev build docx            # DOCX only
+```
+
+## Annotation Syntax (CriticMarkup)
+
+- `{++inserted text++}` - Additions
+- `{--deleted text--}` - Deletions
+- `{~~old~>new~~}` - Substitutions
+- `{>>Author: comment<<}` - Comments
+
+## Cross-References
+
+Use dynamic references in markdown:
+- `@fig:label` - Figure reference (becomes "Figure 1" in Word)
+- `@tbl:label` - Table reference
+- `{#fig:label}` - Anchor for figures
+
+## Project Structure
+
+- `rev.yaml` - Project configuration
+- `*.md` - Section files (introduction.md, methods.md, etc.)
+- `paper.md` - Combined output (generated by build)
+- `figures/` - Images directory
+
+### DOI Management
+```bash
+rev doi check references.bib     # Validate DOIs (Crossref + DataCite)
+rev doi lookup references.bib    # Find missing DOIs by title/author/year
+rev doi fetch <doi>              # Get BibTeX from DOI
+rev doi add <doi>                # Add citation to .bib file
+```
+
+Options:
+- `--confidence low|medium|high` - Filter lookup results by confidence
+- `--strict` - Fail if articles are missing DOIs
+- Skip entries: add `nodoi = {true}` or `% no-doi` comment before entry
+
+## Workflow Tips
+
+1. When user imports a reviewed Word doc, help them go through comments
+2. Use `rev reply` to respond to each comment as you address it
+3. After addressing all comments, run `rev build docx` to generate updated Word doc
+4. Use `rev doi check` to validate bibliography before submission

package/README.md

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+# docrev
+
+[![npm](https://img.shields.io/npm/v/docrev)](https://www.npmjs.com/package/docrev)
+
+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.
+
+## Install
+
+```bash
+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))
+
+```bash
+# macOS
+brew install pandoc pandoc-crossref
+
+# Ubuntu/Debian
+sudo apt install pandoc
+
+# Windows
+winget install JohnMacFarlane.Pandoc
+```
+
+Verify installation:
+```bash
+rev --version
+rev install    # Check for missing dependencies
+```
+
+## 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 and filter reviewer comments
+- **DOI validation** - Check and find DOIs via Crossref/DataCite APIs
+- **Cross-reference conversion** - Auto-convert hardcoded "Figure 1" to dynamic `@fig:label` syntax
+
+## 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
+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
+
+# Build PDF and Word
+rev build
+
+# Build specific format
+rev build pdf
+rev build docx
+rev build tex
+rev build all    # PDF + DOCX + TEX
+```
+
+### Review Workflow
+
+```bash
+# Import reviewer's Word doc to section files
+rev sections reviewed.docx
+
+# Review track changes interactively
+rev review methods.md
+
+# See remaining comments
+rev comments methods.md
+
+# Rebuild
+rev build docx
+```
+
+## Commands
+
+### Build & Create
+
+| Command | Description |
+|---------|-------------|
+| `rev build [formats...]` | Build PDF/DOCX/TEX from sections |
+| `rev new <name>` | Create new project from template |
+| `rev new --list` | List available templates |
+| `rev install` | Check/install dependencies (pandoc-crossref) |
+
+### Import & Export
+
+| 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 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 |
+
+### 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) |
+
+## Project Structure
+
+A typical rev project:
+
+```
+my-paper/
+├── rev.yaml           # Project 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
+
+docx:
+  reference: template.docx   # Optional reference doc
+  keepComments: true
+```
+
+## Annotation Syntax (CriticMarkup)
+
+```markdown
+{++inserted text++}      # Insertions
+{--deleted text--}       # Deletions
+{~~old~>new~~}           # Substitutions
+{>>Author: comment<<}    # Comments
+```
+
+## 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.
+```
+
+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`
+
+## 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
+
+- 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
+
+## License
+
+MIT