docrev 0.9.13 → 0.9.14

package/skill/REFERENCE.md

@@ -1,431 +1,431 @@
-# docrev Command Reference
-
-## Project Creation
-
-### rev new
-Create a new document project.
-```bash
-rev new my-document          # Creates my-document/ with section files
-rev new my-document --template apa
-```
-
-## Document Import/Export
-
-### rev import
-Import a Word document with track changes and comments.
-```bash
-rev import manuscript.docx
-rev import manuscript.docx --output ./project
-```
-
-### rev sync
-Sync feedback from a reviewed Word document into existing markdown sections.
-```bash
-rev sync reviewed.docx          # Updates markdown with track changes/comments
-rev sync                        # Auto-detect most recent .docx
-rev sync reviewed.docx methods  # Sync only methods section
-rev sync reviewed.docx --comments-only  # Insert comments only; never modify prose
-```
-
-`--comments-only` skips the Word→Markdown diff entirely. Use it when the
-markdown has been revised between sending the docx out for review and
-receiving it back: applying track changes from a stale draft would clobber
-newer edits, but comments still need to land. Comments are placed at
-fuzzy-matched anchors against the current prose. Pair with
-`rev verify-anchors` to see which ones won't fit before you run sync.
-
-### rev verify-anchors
-Report drift between Word comment anchors and the current markdown.
-```bash
-rev verify-anchors reviewed.docx       # Print per-comment match quality
-rev verify-anchors reviewed.docx --json  # Machine-readable report
-```
-
-Each comment is classified by how well its anchor still matches the current
-section prose:
-
-- `clean` – exact or whitespace-normalized hit
-- `drift` – anchor only matches via stripped-CriticMarkup or partial-prefix fallbacks
-- `context-only` – anchor text is gone, only surrounding context survives
-- `ambiguous` – multiple candidate positions; needs context to disambiguate
-- `unmatched` – nothing maps; user must place the comment manually
-
-Useful before `rev sync --comments-only` to plan which comments will land
-automatically and which need manual placement.
-
-### 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 build docx --dual        # Clean + annotated versions
-```
-
-The `--dual` flag produces:
-- `paper.docx` — clean, for submission
-- `paper_comments.docx` — includes comment threads as Word comments
-
-### 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 project overview or annotation counts for a file.
-```bash
-rev status               # Project overview (words, comments, changes)
-rev status methods.md    # Specific file annotations
-```
-
-### rev next / rev prev
-Navigate pending comments.
-```bash
-rev next                 # Show next pending comment
-rev next -n 3            # Show 3rd pending comment
-rev prev                 # Show last pending comment
-rev first methods        # First comment in methods section
-rev last                 # Last comment overall
-```
-
-### rev todo
-List all pending comments as a checklist.
-```bash
-rev todo                 # List all pending
-rev todo --by-author     # Group by author
-```
-
-### rev accept / rev reject
-Accept or reject track changes.
-```bash
-rev accept methods.md         # List all changes
-rev accept methods.md -n 1    # Accept change #1
-rev accept methods.md -a      # Accept all
-rev reject methods.md -n 2    # Reject change #2
-```
-
-### rev archive
-Archive reviewer .docx files.
-```bash
-rev archive              # Move all .docx to archive/
-rev archive --by Smith   # Specify reviewer name
-rev archive --dry-run    # Preview without moving
-```
-
-### 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 22 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 (Layout Workflow)
-
-### 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 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
-```
-
-## rev.yaml Settings
-
-### Tables
-
-Configure table formatting for PDF output:
-
-```yaml
-tables:
-  nowrap:
-    - Prior           # Column headers to keep on one line
-    - "$\\widehat{R}$"
-```
-
-In `nowrap` columns, distribution notation is auto-converted to LaTeX math:
-- `Normal(0, 0.5)` → `$\mathcal{N}(0, 0.5)$`
-- `Student-t(3, 0, 1)` → `$t_3(0, 1)$`
-- `Gamma(2, 0.5)` → `$\text{Gamma}(2, 0.5)$`
-- `Half-Normal(0, 1)` → `$\text{Half-Normal}(0, 1)$`
-- `Exponential(1)` → `$\text{Exp}(1)$`
-
-**Tip:** For complex tables, use simple tables (space-aligned with dashes) instead of pipe tables to avoid column width issues:
-
-```markdown
-  Parameter    Prior                       Description
-  ----------   -------------------------   ------------------
-  alpha        $\mathcal{N}(0, 0.5)$       Intercept prior
-  beta         $t_3(0, 2.5)$               Slope prior
-```
-
-### Postprocess Scripts
-
-Run custom scripts after output generation:
-
-```yaml
-postprocess:
-  pdf: ./scripts/fix-pdf.py      # Runs after PDF
-  docx: ./scripts/add-meta.js    # Runs after DOCX
-  tex: ./scripts/tweak-latex.sh  # Runs after TEX
-  pptx: ./scripts/fix-slides.ps1 # Runs after PPTX
-  all: ./scripts/notify.js       # Runs after ANY format
-```
-
-**Environment variables** available to scripts:
-
-| Variable | Description |
-|----------|-------------|
-| `OUTPUT_FILE` | Full path to generated file |
-| `OUTPUT_FORMAT` | Format: `pdf`, `docx`, `tex`, `pptx`, `beamer` |
-| `PROJECT_DIR` | Directory containing rev.yaml |
-| `CONFIG_PATH` | Full path to rev.yaml |
-
-**Supported script types:** `.js`, `.mjs` (Node), `.py` (Python), `.ps1` (PowerShell), `.sh` (Bash)
-
-**Example Python script** (add DOCX metadata):
-```python
-import os
-from docx import Document
-doc = Document(os.environ['OUTPUT_FILE'])
-doc.core_properties.author = "Research Team"
-doc.save(os.environ['OUTPUT_FILE'])
-```
-
-Use `--verbose` flag to see script output:
-```bash
-rev build pdf --verbose
-```
-
-## Shell Completions
-
-### rev completions
-Output shell completions.
-```bash
-eval "$(rev completions bash)"  # Bash
-eval "$(rev completions zsh)"   # Zsh
-```
-
-## AI Skill Installation
-
-### rev install-cli-skill
-Install the docrev skill for AI coding assistants.
-```bash
-rev install-cli-skill        # Install to ~/.claude/skills/docrev
-```
-
-### rev uninstall-cli-skill
-Remove the installed skill.
-```bash
-rev uninstall-cli-skill
-```
+# docrev Command Reference
+
+## Project Creation
+
+### rev new
+Create a new document project.
+```bash
+rev new my-document          # Creates my-document/ with section files
+rev new my-document --template apa
+```
+
+## Document Import/Export
+
+### rev import
+Import a Word document with track changes and comments.
+```bash
+rev import manuscript.docx
+rev import manuscript.docx --output ./project
+```
+
+### rev sync
+Sync feedback from a reviewed Word document into existing markdown sections.
+```bash
+rev sync reviewed.docx          # Updates markdown with track changes/comments
+rev sync                        # Auto-detect most recent .docx
+rev sync reviewed.docx methods  # Sync only methods section
+rev sync reviewed.docx --comments-only  # Insert comments only; never modify prose
+```
+
+`--comments-only` skips the Word→Markdown diff entirely. Use it when the
+markdown has been revised between sending the docx out for review and
+receiving it back: applying track changes from a stale draft would clobber
+newer edits, but comments still need to land. Comments are placed at
+fuzzy-matched anchors against the current prose. Pair with
+`rev verify-anchors` to see which ones won't fit before you run sync.
+
+### rev verify-anchors
+Report drift between Word comment anchors and the current markdown.
+```bash
+rev verify-anchors reviewed.docx       # Print per-comment match quality
+rev verify-anchors reviewed.docx --json  # Machine-readable report
+```
+
+Each comment is classified by how well its anchor still matches the current
+section prose:
+
+- `clean` – exact or whitespace-normalized hit
+- `drift` – anchor only matches via stripped-CriticMarkup or partial-prefix fallbacks
+- `context-only` – anchor text is gone, only surrounding context survives
+- `ambiguous` – multiple candidate positions; needs context to disambiguate
+- `unmatched` – nothing maps; user must place the comment manually
+
+Useful before `rev sync --comments-only` to plan which comments will land
+automatically and which need manual placement.
+
+### 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 build docx --dual        # Clean + annotated versions
+```
+
+The `--dual` flag produces:
+- `paper.docx` — clean, for submission
+- `paper_comments.docx` — includes comment threads as Word comments
+
+### 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 project overview or annotation counts for a file.
+```bash
+rev status               # Project overview (words, comments, changes)
+rev status methods.md    # Specific file annotations
+```
+
+### rev next / rev prev
+Navigate pending comments.
+```bash
+rev next                 # Show next pending comment
+rev next -n 3            # Show 3rd pending comment
+rev prev                 # Show last pending comment
+rev first methods        # First comment in methods section
+rev last                 # Last comment overall
+```
+
+### rev todo
+List all pending comments as a checklist.
+```bash
+rev todo                 # List all pending
+rev todo --by-author     # Group by author
+```
+
+### rev accept / rev reject
+Accept or reject track changes.
+```bash
+rev accept methods.md         # List all changes
+rev accept methods.md -n 1    # Accept change #1
+rev accept methods.md -a      # Accept all
+rev reject methods.md -n 2    # Reject change #2
+```
+
+### rev archive
+Archive reviewer .docx files.
+```bash
+rev archive              # Move all .docx to archive/
+rev archive --by Smith   # Specify reviewer name
+rev archive --dry-run    # Preview without moving
+```
+
+### 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 22 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 (Layout Workflow)
+
+### 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 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
+```
+
+## rev.yaml Settings
+
+### Tables
+
+Configure table formatting for PDF output:
+
+```yaml
+tables:
+  nowrap:
+    - Prior           # Column headers to keep on one line
+    - "$\\widehat{R}$"
+```
+
+In `nowrap` columns, distribution notation is auto-converted to LaTeX math:
+- `Normal(0, 0.5)` → `$\mathcal{N}(0, 0.5)$`
+- `Student-t(3, 0, 1)` → `$t_3(0, 1)$`
+- `Gamma(2, 0.5)` → `$\text{Gamma}(2, 0.5)$`
+- `Half-Normal(0, 1)` → `$\text{Half-Normal}(0, 1)$`
+- `Exponential(1)` → `$\text{Exp}(1)$`
+
+**Tip:** For complex tables, use simple tables (space-aligned with dashes) instead of pipe tables to avoid column width issues:
+
+```markdown
+  Parameter    Prior                       Description
+  ----------   -------------------------   ------------------
+  alpha        $\mathcal{N}(0, 0.5)$       Intercept prior
+  beta         $t_3(0, 2.5)$               Slope prior
+```
+
+### Postprocess Scripts
+
+Run custom scripts after output generation:
+
+```yaml
+postprocess:
+  pdf: ./scripts/fix-pdf.py      # Runs after PDF
+  docx: ./scripts/add-meta.js    # Runs after DOCX
+  tex: ./scripts/tweak-latex.sh  # Runs after TEX
+  pptx: ./scripts/fix-slides.ps1 # Runs after PPTX
+  all: ./scripts/notify.js       # Runs after ANY format
+```
+
+**Environment variables** available to scripts:
+
+| Variable | Description |
+|----------|-------------|
+| `OUTPUT_FILE` | Full path to generated file |
+| `OUTPUT_FORMAT` | Format: `pdf`, `docx`, `tex`, `pptx`, `beamer` |
+| `PROJECT_DIR` | Directory containing rev.yaml |
+| `CONFIG_PATH` | Full path to rev.yaml |
+
+**Supported script types:** `.js`, `.mjs` (Node), `.py` (Python), `.ps1` (PowerShell), `.sh` (Bash)
+
+**Example Python script** (add DOCX metadata):
+```python
+import os
+from docx import Document
+doc = Document(os.environ['OUTPUT_FILE'])
+doc.core_properties.author = "Research Team"
+doc.save(os.environ['OUTPUT_FILE'])
+```
+
+Use `--verbose` flag to see script output:
+```bash
+rev build pdf --verbose
+```
+
+## Shell Completions
+
+### rev completions
+Output shell completions.
+```bash
+eval "$(rev completions bash)"  # Bash
+eval "$(rev completions zsh)"   # Zsh
+```
+
+## AI Skill Installation
+
+### rev install-cli-skill
+Install the docrev skill for AI coding assistants.
+```bash
+rev install-cli-skill        # Install to ~/.claude/skills/docrev
+```
+
+### rev uninstall-cli-skill
+Remove the installed skill.
+```bash
+rev uninstall-cli-skill
+```