docrev 0.11.1 → 0.11.2

package/README.md

@@ -1,433 +1,433 @@
-# docrev
-
-[![npm](https://img.shields.io/npm/v/docrev)](https://www.npmjs.com/package/docrev)
-[![npm downloads](https://img.shields.io/npm/dm/docrev)](https://www.npmjs.com/package/docrev)
-[![node](https://img.shields.io/node/v/docrev)](https://nodejs.org)
-[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
-[![CI](https://github.com/gcol33/docrev/actions/workflows/ci.yml/badge.svg)](https://github.com/gcol33/docrev/actions/workflows/ci.yml)
-
-A CLI for writing documents in Markdown while collaborating with Word users.
-
-Write in `.md` files under version control; build Word or PDF when you need to share. When reviewers return their annotated copy, `rev sync` pulls the feedback into your markdown sections, where you reply to comments, accept or reject changes, and rebuild. Equations, figures, citations, and cross-references survive both directions.
-
-## The Problem
-
-After a few rounds of feedback, the project directory looks like this:
-
-```
-manuscript_v1.docx
-manuscript_v2_john_comments.docx
-manuscript_v2_jane_comments.docx
-manuscript_v3_merged_final.docx
-manuscript_v3_merged_final_REAL.docx
-manuscript_v3_merged_final_REAL_submitted.docx
-```
-
-By the third filename, the document has split. One file has Jane's comments, another has John's track changes, a third has your reconciliation, and which one is current depends on what you remember. Reconciliation takes an afternoon and goes wrong every time the Word formatting drifts.
-
-docrev keeps the markdown as the canonical version, under git. The DOCX is rebuilt each time you share; reviewer comments and track changes come back into your section files when you sync, where you reply to or accept them in the terminal.
-
-## Highlights
-
-- **Markdown → Word/PDF** with citations, figures, equations, cross-references
-- **Round-trip sync**: import Word track changes and comments back to Markdown
-- **CLI review workflow**: reply to comments, accept/reject changes from terminal
-- **DOI tools**: validate, lookup, and auto-add references from DOIs
-- **21 journal styles**: Nature, Science, PNAS, and more
-- **Version control friendly**: plain text source, full git history
-
-## Install
-
-```bash
-npm install -g docrev
-```
-
-Requires [Node.js](https://nodejs.org) 18+. Building DOCX or PDF needs [Pandoc](https://pandoc.org). For complex PDFs (math, cross-references, journal styles), [LaTeX](#installing-dependencies) is also needed; simpler documents can build through pandoc alone with a non-LaTeX engine (e.g. `pdf.engine: typst` in `rev.yaml`).
-
-## Quick Example
-
-Write in Markdown with citations and cross-references:
-
-```markdown
-Climate change poses significant challenges [@IPCC2021]. As shown in
-@fig:temperature, global temperatures have risen steadily.
-
-![Temperature anomalies](figures/temperature.png){#fig:temperature}
-
-The relationship follows $\Delta T = \lambda \cdot \Delta F$ (@eq:forcing).
-```
-
-Build and share:
-
-```bash
-rev build docx    # → output/paper.docx
-rev build pdf     # → output/paper.pdf
-```
-
-When collaborators return the Word doc with track changes:
-
-```bash
-rev sync reviewed.docx    # their comments → your markdown
-```
-
-## How It Works
-
-```
-┌─────────────┐     rev build docx      ┌─────────────┐
-│             │ ───────────────────────→│             │
-│  Markdown   │                         │    Word     │  → collaborators
-│   (you)     │     rev build pdf       │   / PDF     │  → journals
-│             │ ───────────────────────→│             │
-└─────────────┘                         └─────────────┘
-       ↑                                       │
-       │              rev sync                 │
-       └───────────────────────────────────────┘
-              their feedback → your files
-```
-
-## What's in a Project
-
-`rev new my-paper` creates the project. It prompts for the section names (default: `introduction, methods, results, discussion`) or accepts them up front via `-s intro,methods,results,discussion`. Each name becomes its own `.md` file. (`rev import some.docx` is the other entry point — it splits an existing Word document into one section per top-level heading.)
-
-```
-my-paper/
-├── rev.yaml          ← config: title, authors, section order, journal profile
-├── intro.md          ← section files; named at creation, one per section
-├── methods.md
-├── results.md
-├── discussion.md
-├── references.bib    ← BibTeX bibliography
-├── figures/          ← images referenced from sections
-├── paper.md          ← auto-combined source, regenerated each build
-└── output/           ← built artefacts (docx, pdf, tex)
-    ├── my-paper.docx
-    └── my-paper.pdf
-```
-
-You edit the section files and the config; everything else is generated. `paper.md` is rebuilt from the section files in the order set by `rev.yaml`, and `output/` holds whatever the last build produced. After `rev sync`, comments and track changes from the reviewer's Word file appear inline in the section files as CriticMarkup annotations. Set `outputDir: null` in `rev.yaml` if you'd rather have outputs land alongside `paper.md`.
-
-To set your own per-user default sections so future `rev new` calls skip the prompt:
-
-```bash
-rev config sections "intro,methods,results,discussion"
-```
-
-## The CLI Review Cycle
-
-When reviewers send back a Word document with track changes and comments:
-
-```bash
-rev sync reviewed.docx            # import feedback into markdown
-```
-
-Track changes appear inline - accept or reject by editing:
-
-```markdown
-The sample size was {--100--}{++150++} participants.
-```
-
-Handle comments without opening Word:
-
-```bash
-rev comments                      # list all comments
-rev reply methods.md -n 1 -m "Added clarification"
-rev resolve methods.md -n 1       # mark as resolved
-rev build docx --dual             # clean + annotated versions
-rev build docx --dual --show-changes  # one file: tracked changes + threaded comments
-```
-
-PDF annotations work the same way:
-
-```bash
-rev sync annotated.pdf
-rev pdf-comments annotated.pdf --append methods.md
-```
-
-When several reviewers return separate files, `rev merge` reconciles them:
-
-```bash
-rev merge reviewer_A.docx reviewer_B.docx
-```
-
-Each reviewer's file is compared against `.rev/base.docx` (auto-saved on every build) to isolate that reviewer's changes; conflicts on the same passage are flagged for interactive resolution.
-
-## Getting Started
-
-### Starting a New Document
-
-Create a new project:
-
-```bash
-rev new my-report
-cd my-report
-```
-
-You'll be prompted to enter your section names, or press Enter to use the default structure. You can also specify sections directly:
-
-```bash
-rev new my-report -s intro,methods,results,discussion
-```
-
-Or set your preferred default sections once:
-
-```bash
-rev config sections "intro,methods,results,discussion"
-```
-
-This creates the project folder with your section files — edit them, then build:
-
-```bash
-rev build docx pdf
-```
-
-The output filename comes from `title` in `rev.yaml`. Citations are resolved, equations rendered, and cross-references numbered. The directory layout is described above in [What's in a Project](#whats-in-a-project).
-
-### Starting from an Existing Word Document
-
-If you have a Word document to convert:
-
-```bash
-rev import manuscript.docx
-```
-
-This creates a project folder and splits the document into section files. Images are extracted to `figures/`, equations are converted to LaTeX, and track changes/comments are preserved as markdown annotations.
-
-### Configuration
-
-Layout is controlled in `rev.yaml`:
-
-```yaml
-title: "My Document"
-authors: []
-sections:
-  - intro.md
-  - methods.md
-  - results.md
-  - discussion.md
-
-# Where built artefacts land (default: output/). Set to null for the
-# legacy "outputs alongside paper.md" layout.
-outputDir: output
-
-docx:
-  reference: template.docx       # your Word template
-
-pdf:
-  documentclass: article
-  fontsize: 12pt
-  engine: pdflatex               # or xelatex/lualatex for Latin-Extended
-  # Fonts apply only under xelatex/lualatex (fontspec):
-  # mainfont: "TeX Gyre Termes"
-  # sansfont: "TeX Gyre Heros"
-  # monofont: "TeX Gyre Cursor"
-```
-
-Switch to `engine: xelatex` (or `lualatex`) when the manuscript has Czech/Polish/Croatian/Spanish names or species epithets that `pdflatex` mangles. Under those engines, `mainfont`/`sansfont`/`monofont` are forwarded to pandoc.
-
-Configure your name for comment replies:
-
-```bash
-rev config user "Your Name"
-```
-
-### Table Formatting
-
-For PDF output, configure columns that should not wrap:
-
-```yaml
-tables:
-  nowrap:
-    - Prior              # column headers to keep on one line
-    - "$\\widehat{R}$"
-```
-
-Distribution notation in nowrap columns is auto-converted to LaTeX math:
-`Normal(0, 0.5)` → `$\mathcal{N}(0, 0.5)$`
-
-### Placeholder Macros
-
-Mark unfinished spots in a draft with `\tofill{X}` and they highlight as bold
-orange `[X]` in every output format:
-
-```markdown
-We collected data from \tofill{N sites} between \tofill{date range}.
-```
-
-The macro works in DOCX, PDF, TeX, Beamer, and HTML without any per-project
-filter setup. Add custom macros (e.g. `\note`, `\citeNeeded`) under `macros:`
-in `rev.yaml`:
-
-```yaml
-macros:
-  - name: note
-    default:
-      color: "1E40AF"      # 6-digit hex, no '#'
-      bold: true
-      prefix: "NOTE: "
-```
-
-See [docs/configuration.md](docs/configuration.md) for the full schema and
-per-format overrides.
-
-### Postprocess Scripts
-
-Run custom scripts after output generation:
-
-```yaml
-postprocess:
-  pdf: ./scripts/fix-tables.py    # runs after PDF
-  docx: ./scripts/add-meta.js     # runs after DOCX
-  all: ./scripts/notify.sh        # runs after any format
-```
-
-Scripts receive environment variables: `OUTPUT_FILE`, `OUTPUT_FORMAT`, `PROJECT_DIR`, `CONFIG_PATH`.
-
-Use `--verbose` to see script output:
-
-```bash
-rev build pdf --verbose
-```
-
-### Journal Profiles
-
-Journal profiles provide both validation rules and build formatting defaults. Set in `rev.yaml`:
-
-```yaml
-journal: nature
-```
-
-Or pass on the command line:
-
-```bash
-rev build pdf -j nature     # applies Nature's CSL style + PDF settings
-```
-
-When a journal is set, its formatting defaults (CSL citation style, font size, margins, line spacing) are applied automatically. Your explicit `rev.yaml` settings always take priority.
-
-Six profiles include formatting: `nature`, `science`, `cell`, `pnas`, `plos-one`, `elife`. All 21 profiles support validation. Custom profiles can include formatting too — see [docs/configuration.md](docs/configuration.md).
-
-```bash
-rev validate --list          # see all profiles ([formatting] tag = build support)
-rev profiles --fetch-csl apa # download a CSL style to cache
-rev profiles --list-csl      # list cached CSL styles
-```
-
-## Annotation Syntax
-
-Track changes from Word appear as [CriticMarkup](http://criticmarkup.com/):
-
-```markdown
-The sample size was {--100--}{++150++} participants.   # deletion + insertion
-Data was collected {~~monthly~>weekly~~}.              # substitution
-{>>Reviewer 2: Please clarify.<<}                      # comment
-```
-
-## Writing Tips
-
-Track word count changes between versions:
-
-```bash
-rev diff                    # compare against last commit
-#  methods.md     +142 words  -38 words
-#  results.md      +89 words  -12 words
-```
-
-Add references to `references.bib` (BibTeX format):
-
-```bibtex
-@article{Smith2020,
-  author = {Smith, Jane},
-  title = {Paper Title},
-  journal = {Nature},
-  year = {2020},
-  doi = {10.1038/example}
-}
-```
-
-Cite with `[@Smith2020]` or `[@Smith2020; @Jones2021]` for multiple sources.
-
-Equations use LaTeX: inline `$E = mc^2$` or display `$$\sum_{i=1}^{n} x_i$$`.
-
-Cross-references: `@fig:label`, `@tbl:label`, `@eq:label` → "Figure 1", "Table 2", "Equation 3".
-
-## Command Reference
-
-| Task | Command |
-|------|---------|
-| Create project | `rev new my-project` |
-| Create LaTeX project | `rev new my-project --template latex` |
-| Import Word document | `rev import manuscript.docx` |
-| Extract Word equations | `rev equations from-word doc.docx` |
-| Build DOCX | `rev build docx` |
-| Build PDF | `rev build pdf` |
-| Build clean + annotated | `rev build docx --dual` |
-| Build with visible track changes | `rev build docx --show-changes` |
-| Build tracked changes + comments in one file | `rev build docx --dual --show-changes` |
-| Sync Word feedback | `rev sync reviewed.docx` |
-| Sync PDF comments | `rev sync annotated.pdf` |
-| Extract PDF comments | `rev pdf-comments annotated.pdf` |
-| Extract with highlighted text | `rev pdf-comments file.pdf --with-text` |
-| Project status | `rev status` |
-| Next pending comment | `rev next` |
-| List pending comments | `rev todo` |
-| Filter by author | `rev comments file.md --author "Reviewer 2"` |
-| Accept all changes | `rev accept file.md -a` |
-| Reject change | `rev reject file.md -n 1` |
-| Reply to comment | `rev reply file.md -n 1 -m "response"` |
-| Reply to all pending | `rev reply file.md --all -m "Addressed"` |
-| Resolve comment | `rev resolve file.md -n 1` |
-| Show contributors | `rev contributors` |
-| Lookup ORCID | `rev orcid 0000-0002-1825-0097` |
-| Merge reviewer feedback | `rev merge reviewer_A.docx reviewer_B.docx` |
-| Archive reviewer files | `rev archive` |
-| Check DOIs | `rev doi check references.bib` |
-| Find missing DOIs | `rev doi lookup references.bib` |
-| Add citation from DOI | `rev doi add 10.1038/example` |
-| Word count | `rev wc` |
-| Pre-submission check | `rev check` |
-| Check for updates | `rev upgrade --check` |
-
-Run `rev help` to see all commands, or `rev help <command>` for details on a specific command.
-
-Full command reference: [docs/commands.md](docs/commands.md)
-
-## Claude Code Skill
-
-Install the docrev skill for [Claude Code](https://claude.ai/code):
-
-```bash
-rev install-cli-skill      # install to ~/.claude/skills/docrev
-rev uninstall-cli-skill    # remove
-```
-
-Once installed, Claude understands docrev commands and can help navigate comments, draft replies, and manage your revision cycle.
-
-## Installing Dependencies
-
-### Pandoc
-
-[Pandoc](https://pandoc.org) handles document conversion.
-
-| Platform | Command |
-|----------|---------|
-| macOS | `brew install pandoc` |
-| Windows | `winget install JohnMacFarlane.Pandoc` |
-| Debian/Ubuntu | `sudo apt install pandoc` |
-| Fedora | `sudo dnf install pandoc` |
-
-Other platforms: [pandoc.org/installing](https://pandoc.org/installing.html)
-
-### LaTeX (for complex PDF builds)
-
-| Platform | Command |
-|----------|---------|
-| macOS | `brew install --cask mactex` |
-| Windows | `winget install MiKTeX.MiKTeX` |
-| Debian/Ubuntu | `sudo apt install texlive-full` |
-| Fedora | `sudo dnf install texlive-scheme-full` |
-
-Alternatively, [TinyTeX](https://yihui.org/tinytex/) provides a minimal distribution that downloads packages on demand.
-
-## License
-
-MIT
+# docrev
+
+[![npm](https://img.shields.io/npm/v/docrev)](https://www.npmjs.com/package/docrev)
+[![npm downloads](https://img.shields.io/npm/dm/docrev)](https://www.npmjs.com/package/docrev)
+[![node](https://img.shields.io/node/v/docrev)](https://nodejs.org)
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+[![CI](https://github.com/gcol33/docrev/actions/workflows/ci.yml/badge.svg)](https://github.com/gcol33/docrev/actions/workflows/ci.yml)
+
+A CLI for writing documents in Markdown while collaborating with Word users.
+
+Write in `.md` files under version control; build Word or PDF when you need to share. When reviewers return their annotated copy, `rev sync` pulls the feedback into your markdown sections, where you reply to comments, accept or reject changes, and rebuild. Equations, figures, citations, and cross-references survive both directions.
+
+## The Problem
+
+After a few rounds of feedback, the project directory looks like this:
+
+```
+manuscript_v1.docx
+manuscript_v2_john_comments.docx
+manuscript_v2_jane_comments.docx
+manuscript_v3_merged_final.docx
+manuscript_v3_merged_final_REAL.docx
+manuscript_v3_merged_final_REAL_submitted.docx
+```
+
+By the third filename, the document has split. One file has Jane's comments, another has John's track changes, a third has your reconciliation, and which one is current depends on what you remember. Reconciliation takes an afternoon and goes wrong every time the Word formatting drifts.
+
+docrev keeps the markdown as the canonical version, under git. The DOCX is rebuilt each time you share; reviewer comments and track changes come back into your section files when you sync, where you reply to or accept them in the terminal.
+
+## Highlights
+
+- **Markdown → Word/PDF** with citations, figures, equations, cross-references
+- **Round-trip sync**: import Word track changes and comments back to Markdown
+- **CLI review workflow**: reply to comments, accept/reject changes from terminal
+- **DOI tools**: validate, lookup, and auto-add references from DOIs
+- **21 journal styles**: Nature, Science, PNAS, and more
+- **Version control friendly**: plain text source, full git history
+
+## Install
+
+```bash
+npm install -g docrev
+```
+
+Requires [Node.js](https://nodejs.org) 18+. Building DOCX or PDF needs [Pandoc](https://pandoc.org). For complex PDFs (math, cross-references, journal styles), [LaTeX](#installing-dependencies) is also needed; simpler documents can build through pandoc alone with a non-LaTeX engine (e.g. `pdf.engine: typst` in `rev.yaml`).
+
+## Quick Example
+
+Write in Markdown with citations and cross-references:
+
+```markdown
+Climate change poses significant challenges [@IPCC2021]. As shown in
+@fig:temperature, global temperatures have risen steadily.
+
+![Temperature anomalies](figures/temperature.png){#fig:temperature}
+
+The relationship follows $\Delta T = \lambda \cdot \Delta F$ (@eq:forcing).
+```
+
+Build and share:
+
+```bash
+rev build docx    # → output/paper.docx
+rev build pdf     # → output/paper.pdf
+```
+
+When collaborators return the Word doc with track changes:
+
+```bash
+rev sync reviewed.docx    # their comments → your markdown
+```
+
+## How It Works
+
+```
+┌─────────────┐     rev build docx      ┌─────────────┐
+│             │ ───────────────────────→│             │
+│  Markdown   │                         │    Word     │  → collaborators
+│   (you)     │     rev build pdf       │   / PDF     │  → journals
+│             │ ───────────────────────→│             │
+└─────────────┘                         └─────────────┘
+       ↑                                       │
+       │              rev sync                 │
+       └───────────────────────────────────────┘
+              their feedback → your files
+```
+
+## What's in a Project
+
+`rev new my-paper` creates the project. It prompts for the section names (default: `introduction, methods, results, discussion`) or accepts them up front via `-s intro,methods,results,discussion`. Each name becomes its own `.md` file. (`rev import some.docx` is the other entry point — it splits an existing Word document into one section per top-level heading.)
+
+```
+my-paper/
+├── rev.yaml          ← config: title, authors, section order, journal profile
+├── intro.md          ← section files; named at creation, one per section
+├── methods.md
+├── results.md
+├── discussion.md
+├── references.bib    ← BibTeX bibliography
+├── figures/          ← images referenced from sections
+├── paper.md          ← auto-combined source, regenerated each build
+└── output/           ← built artefacts (docx, pdf, tex)
+    ├── my-paper.docx
+    └── my-paper.pdf
+```
+
+You edit the section files and the config; everything else is generated. `paper.md` is rebuilt from the section files in the order set by `rev.yaml`, and `output/` holds whatever the last build produced. After `rev sync`, comments and track changes from the reviewer's Word file appear inline in the section files as CriticMarkup annotations. Set `outputDir: null` in `rev.yaml` if you'd rather have outputs land alongside `paper.md`.
+
+To set your own per-user default sections so future `rev new` calls skip the prompt:
+
+```bash
+rev config sections "intro,methods,results,discussion"
+```
+
+## The CLI Review Cycle
+
+When reviewers send back a Word document with track changes and comments:
+
+```bash
+rev sync reviewed.docx            # import feedback into markdown
+```
+
+Track changes appear inline - accept or reject by editing:
+
+```markdown
+The sample size was {--100--}{++150++} participants.
+```
+
+Handle comments without opening Word:
+
+```bash
+rev comments                      # list all comments
+rev reply methods.md -n 1 -m "Added clarification"
+rev resolve methods.md -n 1       # mark as resolved
+rev build docx --dual             # clean + annotated versions
+rev build docx --dual --show-changes  # one file: tracked changes + threaded comments
+```
+
+PDF annotations work the same way:
+
+```bash
+rev sync annotated.pdf
+rev pdf-comments annotated.pdf --append methods.md
+```
+
+When several reviewers return separate files, `rev merge` reconciles them:
+
+```bash
+rev merge reviewer_A.docx reviewer_B.docx
+```
+
+Each reviewer's file is compared against `.rev/base.docx` (auto-saved on every build) to isolate that reviewer's changes; conflicts on the same passage are flagged for interactive resolution.
+
+## Getting Started
+
+### Starting a New Document
+
+Create a new project:
+
+```bash
+rev new my-report
+cd my-report
+```
+
+You'll be prompted to enter your section names, or press Enter to use the default structure. You can also specify sections directly:
+
+```bash
+rev new my-report -s intro,methods,results,discussion
+```
+
+Or set your preferred default sections once:
+
+```bash
+rev config sections "intro,methods,results,discussion"
+```
+
+This creates the project folder with your section files — edit them, then build:
+
+```bash
+rev build docx pdf
+```
+
+The output filename comes from `title` in `rev.yaml`. Citations are resolved, equations rendered, and cross-references numbered. The directory layout is described above in [What's in a Project](#whats-in-a-project).
+
+### Starting from an Existing Word Document
+
+If you have a Word document to convert:
+
+```bash
+rev import manuscript.docx
+```
+
+This creates a project folder and splits the document into section files. Images are extracted to `figures/`, equations are converted to LaTeX, and track changes/comments are preserved as markdown annotations.
+
+### Configuration
+
+Layout is controlled in `rev.yaml`:
+
+```yaml
+title: "My Document"
+authors: []
+sections:
+  - intro.md
+  - methods.md
+  - results.md
+  - discussion.md
+
+# Where built artefacts land (default: output/). Set to null for the
+# legacy "outputs alongside paper.md" layout.
+outputDir: output
+
+docx:
+  reference: template.docx       # your Word template
+
+pdf:
+  documentclass: article
+  fontsize: 12pt
+  engine: pdflatex               # or xelatex/lualatex for Latin-Extended
+  # Fonts apply only under xelatex/lualatex (fontspec):
+  # mainfont: "TeX Gyre Termes"
+  # sansfont: "TeX Gyre Heros"
+  # monofont: "TeX Gyre Cursor"
+```
+
+Switch to `engine: xelatex` (or `lualatex`) when the manuscript has Czech/Polish/Croatian/Spanish names or species epithets that `pdflatex` mangles. Under those engines, `mainfont`/`sansfont`/`monofont` are forwarded to pandoc.
+
+Configure your name for comment replies:
+
+```bash
+rev config user "Your Name"
+```
+
+### Table Formatting
+
+For PDF output, configure columns that should not wrap:
+
+```yaml
+tables:
+  nowrap:
+    - Prior              # column headers to keep on one line
+    - "$\\widehat{R}$"
+```
+
+Distribution notation in nowrap columns is auto-converted to LaTeX math:
+`Normal(0, 0.5)` → `$\mathcal{N}(0, 0.5)$`
+
+### Placeholder Macros
+
+Mark unfinished spots in a draft with `\tofill{X}` and they highlight as bold
+orange `[X]` in every output format:
+
+```markdown
+We collected data from \tofill{N sites} between \tofill{date range}.
+```
+
+The macro works in DOCX, PDF, TeX, Beamer, and HTML without any per-project
+filter setup. Add custom macros (e.g. `\note`, `\citeNeeded`) under `macros:`
+in `rev.yaml`:
+
+```yaml
+macros:
+  - name: note
+    default:
+      color: "1E40AF"      # 6-digit hex, no '#'
+      bold: true
+      prefix: "NOTE: "
+```
+
+See [docs/configuration.md](docs/configuration.md) for the full schema and
+per-format overrides.
+
+### Postprocess Scripts
+
+Run custom scripts after output generation:
+
+```yaml
+postprocess:
+  pdf: ./scripts/fix-tables.py    # runs after PDF
+  docx: ./scripts/add-meta.js     # runs after DOCX
+  all: ./scripts/notify.sh        # runs after any format
+```
+
+Scripts receive environment variables: `OUTPUT_FILE`, `OUTPUT_FORMAT`, `PROJECT_DIR`, `CONFIG_PATH`.
+
+Use `--verbose` to see script output:
+
+```bash
+rev build pdf --verbose
+```
+
+### Journal Profiles
+
+Journal profiles provide both validation rules and build formatting defaults. Set in `rev.yaml`:
+
+```yaml
+journal: nature
+```
+
+Or pass on the command line:
+
+```bash
+rev build pdf -j nature     # applies Nature's CSL style + PDF settings
+```
+
+When a journal is set, its formatting defaults (CSL citation style, font size, margins, line spacing) are applied automatically. Your explicit `rev.yaml` settings always take priority.
+
+Six profiles include formatting: `nature`, `science`, `cell`, `pnas`, `plos-one`, `elife`. All 21 profiles support validation. Custom profiles can include formatting too — see [docs/configuration.md](docs/configuration.md).
+
+```bash
+rev validate --list          # see all profiles ([formatting] tag = build support)
+rev profiles --fetch-csl apa # download a CSL style to cache
+rev profiles --list-csl      # list cached CSL styles
+```
+
+## Annotation Syntax
+
+Track changes from Word appear as [CriticMarkup](http://criticmarkup.com/):
+
+```markdown
+The sample size was {--100--}{++150++} participants.   # deletion + insertion
+Data was collected {~~monthly~>weekly~~}.              # substitution
+{>>Reviewer 2: Please clarify.<<}                      # comment
+```
+
+## Writing Tips
+
+Track word count changes between versions:
+
+```bash
+rev diff                    # compare against last commit
+#  methods.md     +142 words  -38 words
+#  results.md      +89 words  -12 words
+```
+
+Add references to `references.bib` (BibTeX format):
+
+```bibtex
+@article{Smith2020,
+  author = {Smith, Jane},
+  title = {Paper Title},
+  journal = {Nature},
+  year = {2020},
+  doi = {10.1038/example}
+}
+```
+
+Cite with `[@Smith2020]` or `[@Smith2020; @Jones2021]` for multiple sources.
+
+Equations use LaTeX: inline `$E = mc^2$` or display `$$\sum_{i=1}^{n} x_i$$`.
+
+Cross-references: `@fig:label`, `@tbl:label`, `@eq:label` → "Figure 1", "Table 2", "Equation 3".
+
+## Command Reference
+
+| Task | Command |
+|------|---------|
+| Create project | `rev new my-project` |
+| Create LaTeX project | `rev new my-project --template latex` |
+| Import Word document | `rev import manuscript.docx` |
+| Extract Word equations | `rev equations from-word doc.docx` |
+| Build DOCX | `rev build docx` |
+| Build PDF | `rev build pdf` |
+| Build clean + annotated | `rev build docx --dual` |
+| Build with visible track changes | `rev build docx --show-changes` |
+| Build tracked changes + comments in one file | `rev build docx --dual --show-changes` |
+| Sync Word feedback | `rev sync reviewed.docx` |
+| Sync PDF comments | `rev sync annotated.pdf` |
+| Extract PDF comments | `rev pdf-comments annotated.pdf` |
+| Extract with highlighted text | `rev pdf-comments file.pdf --with-text` |
+| Project status | `rev status` |
+| Next pending comment | `rev next` |
+| List pending comments | `rev todo` |
+| Filter by author | `rev comments file.md --author "Reviewer 2"` |
+| Accept all changes | `rev accept file.md -a` |
+| Reject change | `rev reject file.md -n 1` |
+| Reply to comment | `rev reply file.md -n 1 -m "response"` |
+| Reply to all pending | `rev reply file.md --all -m "Addressed"` |
+| Resolve comment | `rev resolve file.md -n 1` |
+| Show contributors | `rev contributors` |
+| Lookup ORCID | `rev orcid 0000-0002-1825-0097` |
+| Merge reviewer feedback | `rev merge reviewer_A.docx reviewer_B.docx` |
+| Archive reviewer files | `rev archive` |
+| Check DOIs | `rev doi check references.bib` |
+| Find missing DOIs | `rev doi lookup references.bib` |
+| Add citation from DOI | `rev doi add 10.1038/example` |
+| Word count | `rev wc` |
+| Pre-submission check | `rev check` |
+| Check for updates | `rev upgrade --check` |
+
+Run `rev help` to see all commands, or `rev help <command>` for details on a specific command.
+
+Full command reference: [docs/commands.md](docs/commands.md)
+
+## Claude Code Skill
+
+Install the docrev skill for [Claude Code](https://claude.ai/code):
+
+```bash
+rev install-cli-skill      # install to ~/.claude/skills/docrev
+rev uninstall-cli-skill    # remove
+```
+
+Once installed, Claude understands docrev commands and can help navigate comments, draft replies, and manage your revision cycle.
+
+## Installing Dependencies
+
+### Pandoc
+
+[Pandoc](https://pandoc.org) handles document conversion.
+
+| Platform | Command |
+|----------|---------|
+| macOS | `brew install pandoc` |
+| Windows | `winget install JohnMacFarlane.Pandoc` |
+| Debian/Ubuntu | `sudo apt install pandoc` |
+| Fedora | `sudo dnf install pandoc` |
+
+Other platforms: [pandoc.org/installing](https://pandoc.org/installing.html)
+
+### LaTeX (for complex PDF builds)
+
+| Platform | Command |
+|----------|---------|
+| macOS | `brew install --cask mactex` |
+| Windows | `winget install MiKTeX.MiKTeX` |
+| Debian/Ubuntu | `sudo apt install texlive-full` |
+| Fedora | `sudo dnf install texlive-scheme-full` |
+
+Alternatively, [TinyTeX](https://yihui.org/tinytex/) provides a minimal distribution that downloads packages on demand.
+
+## License
+
+MIT