maestro-flow 0.5.35 → 0.5.37

package/.claude/skills/scholar-latex-organizer/phases/01-extract-analyze.md

@@ -1,228 +1,228 @@
-# Phase 1: Extract & Analyze
-
-## Objective
-
-Extract the template .zip file, inventory all contents, identify the main LaTeX file and conference type, diagnose structural issues, and present a cleanup plan for user approval.
-
-## Input
-
-- `templatePath`: Path to the .zip template file
-- `conferenceInfo`: Conference name or URL (optional)
-
-## Execution
-
-### Step 1.1: Extract Files
-
-Extract the .zip archive to a temporary directory and list all contents.
-
-```bash
-# Create temp extraction directory
-TEMP_DIR=$(mktemp -d)
-echo "Extracting to: $TEMP_DIR"
-
-# Extract the zip file
-unzip -o "$TEMPLATE_PATH" -d "$TEMP_DIR"
-
-# List all extracted files with structure
-find "$TEMP_DIR" -type f | sort
-```
-
-If extraction fails, check file integrity and ask the user to verify or re-download the .zip file.
-
-### Step 1.2: Identify File Types
-
-Categorize all extracted files into groups:
-
-| Category | Extensions | Purpose |
-|----------|-----------|---------|
-| **LaTeX source** | `.tex` | Main content and section files |
-| **Style files** | `.sty`, `.cls` | Document class and style definitions |
-| **Bibliography** | `.bib` | Reference databases |
-| **Images** | `.png`, `.jpg`, `.jpeg`, `.pdf`, `.eps` | Figures and graphics |
-| **Other** | `.txt`, `.md`, `.bat`, `.sh`, etc. | Supporting files |
-
-```bash
-# Categorize files
-echo "=== LaTeX Sources ==="
-find "$TEMP_DIR" -name "*.tex" -type f
-
-echo "=== Style Files ==="
-find "$TEMP_DIR" \( -name "*.sty" -o -name "*.cls" -o -name "*.bst" \) -type f
-
-echo "=== Bibliography ==="
-find "$TEMP_DIR" -name "*.bib" -type f
-
-echo "=== Images ==="
-find "$TEMP_DIR" \( -name "*.png" -o -name "*.jpg" -o -name "*.jpeg" -o -name "*.pdf" -o -name "*.eps" \) -type f
-
-echo "=== Other ==="
-find "$TEMP_DIR" -type f ! \( -name "*.tex" -o -name "*.sty" -o -name "*.cls" -o -name "*.bst" -o -name "*.bib" -o -name "*.png" -o -name "*.jpg" -o -name "*.jpeg" -o -name "*.pdf" -o -name "*.eps" \)
-```
-
-### Step 1.3: Identify Main File
-
-Determine the main LaTeX file using this priority order:
-
-1. **Check common names** (in order):
-   - `main.tex`
-   - `paper.tex`
-   - `document.tex`
-   - `sample-sigconf.tex`
-   - `template.tex`
-   - `manuscript.tex`
-
-2. **Search for `\documentclass`**: If no common name matches, search all .tex files for `\documentclass` declarations.
-
-```bash
-# Check common names first
-for name in main.tex paper.tex document.tex sample-sigconf.tex template.tex manuscript.tex; do
-  found=$(find "$TEMP_DIR" -name "$name" -type f)
-  if [ -n "$found" ]; then
-    echo "Found main file candidate: $found"
-  fi
-done
-
-# Search for \documentclass in all .tex files
-echo "=== Files containing \\documentclass ==="
-grep -rl '\\documentclass' "$TEMP_DIR" --include="*.tex"
-```
-
-3. **Multiple candidates**: If multiple files contain `\documentclass`, present the list to the user and ask which is the main file. Look for clues:
-   - Files that `\input` or `\include` other .tex files are more likely the main file
-   - Files named `sample*` or `example*` are typically examples, not the main file
-   - The file with the most `\input`/`\include` statements is usually the main file
-
-### Step 1.4: Detect Conference Type
-
-Extract the document class and options from the main file's `\documentclass` declaration.
-
-```bash
-# Extract \documentclass line
-grep '\\documentclass' "$MAIN_FILE"
-```
-
-Parse the result to identify:
-
-| Document Class | Conference | Key Options |
-|---------------|-----------|-------------|
-| `acmart` | ACM (KDD, SIGIR, WWW, etc.) | `sigconf`, `anonymous`, `review`, `nonacm` |
-| `cvpr` | CVPR/ICCV | `review` for anonymous |
-| `neurips_2024` / `neurips_2025` | NeurIPS | Year-specific class |
-| `iclr2024_conference` / `iclr2025_conference` | ICLR | Year-specific class |
-| `aaai24` / `aaai25` | AAAI | Year-specific class |
-| `IEEEtran` | IEEE conferences | `conference` option |
-| `article` | Generic | Various options |
-
-Also detect relevant options:
-- `anonymous` -- anonymous submission mode
-- `review` -- review/submission mode
-- `nonacm` -- non-ACM affiliated (used in KDD)
-- `sigconf` -- ACM SIGCONF format
-
-### Step 1.5: Diagnose Issues
-
-Check the template for common problems that need cleanup:
-
-**Disorganized file structure**:
-- Multi-level directory nesting where flat would suffice
-- .tex files scattered across multiple directories
-- Images mixed with source files
-
-**Redundant content**:
-- Files named `sample*`, `example*`, `demo*`, `test*`
-- Multiple versions of the same file
-- Template documentation files (e.g., `acmguide.pdf`)
-
-**Excessive comments**:
-- Instructional comments like `%% DELETE THIS SECTION`
-- Long blocks of commented-out example text
-- Tutorial-style inline comments explaining LaTeX basics
-
-**Missing dependencies**:
-- .sty or .cls files referenced in `\usepackage` or `\documentclass` but not present in the archive
-- Check `\RequirePackage` statements in .cls files
-
-**Incorrect reference paths**:
-- `\includegraphics` paths that reference non-existent locations
-- `\input` or `\include` paths that would break after reorganization
-- `\bibliography` path mismatches
-
-```bash
-# Check for redundant files
-echo "=== Potential Redundant Files ==="
-find "$TEMP_DIR" -type f \( -name "sample*" -o -name "example*" -o -name "demo*" -o -name "test*" \) | grep -i '\.tex$'
-
-# Check for excessive comments (instructional markers)
-echo "=== Instructional Comment Markers ==="
-grep -rn 'DELETE\|REMOVE\|TODO.*delete\|Replace this\|Your .* here' "$TEMP_DIR" --include="*.tex" | head -20
-
-# Check referenced packages
-echo "=== Referenced Packages ==="
-grep -rh '\\usepackage' "$MAIN_FILE" | sed 's/.*{\(.*\)}.*/\1/' | sort -u
-
-# Check image references
-echo "=== Image References ==="
-grep -rh '\\includegraphics' "$MAIN_FILE" | head -20
-```
-
-### Step 1.6: Present Analysis
-
-Present the complete analysis to the user in a structured format:
-
-```
-=== Template Analysis ===
-
-1. File Inventory:
-   - LaTeX sources: N files
-   - Style files: N files (.sty/.cls/.bst)
-   - Bibliography: N files
-   - Images: N files
-   - Other: N files
-   - Total: N files
-
-2. Main File: [filename]
-   - Document class: [class] with options [options]
-
-3. Conference: [detected conference name]
-   - Type: [submission/camera-ready]
-   - Anonymous: [yes/no]
-
-4. Issues Found:
-   - [x] Disorganized structure: [details]
-   - [x] Redundant files: [list]
-   - [x] Excessive comments: [count] instructional markers
-   - [ ] Missing dependencies: none
-   - [x] Path issues: [details]
-
-5. Proposed Cleanup Plan:
-   a. Create clean directory structure (main.tex, text/, figures/, tables/, styles/)
-   b. Extract and clean main.tex (remove examples, keep config)
-   c. Create section files in text/
-   d. Copy style files to styles/
-   e. Copy images to figures/
-   f. Consolidate bibliography to references.bib
-   g. Remove [N] redundant files
-
-Proceed with cleanup? (Y/n)
-```
-
-Wait for user confirmation before proceeding to Phase 2.
-
-## Output
-
-`analysisResult` object containing:
-
-| Field | Type | Description |
-|-------|------|-------------|
-| `fileInventory` | object | Categorized file lists (tex, sty, bib, images, other) |
-| `mainFile` | string | Path to identified main .tex file |
-| `conferenceType` | object | `{class, options, conference, anonymous}` |
-| `issues` | array | List of diagnosed issues with severity |
-| `approvedPlan` | boolean | Whether user approved the cleanup plan |
-| `tempDir` | string | Path to temporary extraction directory |
-
-## Next Phase
-
-Phase 2: Cleanup & Organize (`phases/02-cleanup-organize.md`)
-- Receives: `analysisResult`, `sectionStructure`, `outputDir`
-- Creates the clean directory structure and reorganizes files
+# Phase 1: Extract & Analyze
+
+## Objective
+
+Extract the template .zip file, inventory all contents, identify the main LaTeX file and conference type, diagnose structural issues, and present a cleanup plan for user approval.
+
+## Input
+
+- `templatePath`: Path to the .zip template file
+- `conferenceInfo`: Conference name or URL (optional)
+
+## Execution
+
+### Step 1.1: Extract Files
+
+Extract the .zip archive to a temporary directory and list all contents.
+
+```bash
+# Create temp extraction directory
+TEMP_DIR=$(mktemp -d)
+echo "Extracting to: $TEMP_DIR"
+
+# Extract the zip file
+unzip -o "$TEMPLATE_PATH" -d "$TEMP_DIR"
+
+# List all extracted files with structure
+find "$TEMP_DIR" -type f | sort
+```
+
+If extraction fails, check file integrity and ask the user to verify or re-download the .zip file.
+
+### Step 1.2: Identify File Types
+
+Categorize all extracted files into groups:
+
+| Category | Extensions | Purpose |
+|----------|-----------|---------|
+| **LaTeX source** | `.tex` | Main content and section files |
+| **Style files** | `.sty`, `.cls` | Document class and style definitions |
+| **Bibliography** | `.bib` | Reference databases |
+| **Images** | `.png`, `.jpg`, `.jpeg`, `.pdf`, `.eps` | Figures and graphics |
+| **Other** | `.txt`, `.md`, `.bat`, `.sh`, etc. | Supporting files |
+
+```bash
+# Categorize files
+echo "=== LaTeX Sources ==="
+find "$TEMP_DIR" -name "*.tex" -type f
+
+echo "=== Style Files ==="
+find "$TEMP_DIR" \( -name "*.sty" -o -name "*.cls" -o -name "*.bst" \) -type f
+
+echo "=== Bibliography ==="
+find "$TEMP_DIR" -name "*.bib" -type f
+
+echo "=== Images ==="
+find "$TEMP_DIR" \( -name "*.png" -o -name "*.jpg" -o -name "*.jpeg" -o -name "*.pdf" -o -name "*.eps" \) -type f
+
+echo "=== Other ==="
+find "$TEMP_DIR" -type f ! \( -name "*.tex" -o -name "*.sty" -o -name "*.cls" -o -name "*.bst" -o -name "*.bib" -o -name "*.png" -o -name "*.jpg" -o -name "*.jpeg" -o -name "*.pdf" -o -name "*.eps" \)
+```
+
+### Step 1.3: Identify Main File
+
+Determine the main LaTeX file using this priority order:
+
+1. **Check common names** (in order):
+   - `main.tex`
+   - `paper.tex`
+   - `document.tex`
+   - `sample-sigconf.tex`
+   - `template.tex`
+   - `manuscript.tex`
+
+2. **Search for `\documentclass`**: If no common name matches, search all .tex files for `\documentclass` declarations.
+
+```bash
+# Check common names first
+for name in main.tex paper.tex document.tex sample-sigconf.tex template.tex manuscript.tex; do
+  found=$(find "$TEMP_DIR" -name "$name" -type f)
+  if [ -n "$found" ]; then
+    echo "Found main file candidate: $found"
+  fi
+done
+
+# Search for \documentclass in all .tex files
+echo "=== Files containing \\documentclass ==="
+grep -rl '\\documentclass' "$TEMP_DIR" --include="*.tex"
+```
+
+3. **Multiple candidates**: If multiple files contain `\documentclass`, present the list to the user and ask which is the main file. Look for clues:
+   - Files that `\input` or `\include` other .tex files are more likely the main file
+   - Files named `sample*` or `example*` are typically examples, not the main file
+   - The file with the most `\input`/`\include` statements is usually the main file
+
+### Step 1.4: Detect Conference Type
+
+Extract the document class and options from the main file's `\documentclass` declaration.
+
+```bash
+# Extract \documentclass line
+grep '\\documentclass' "$MAIN_FILE"
+```
+
+Parse the result to identify:
+
+| Document Class | Conference | Key Options |
+|---------------|-----------|-------------|
+| `acmart` | ACM (KDD, SIGIR, WWW, etc.) | `sigconf`, `anonymous`, `review`, `nonacm` |
+| `cvpr` | CVPR/ICCV | `review` for anonymous |
+| `neurips_2024` / `neurips_2025` | NeurIPS | Year-specific class |
+| `iclr2024_conference` / `iclr2025_conference` | ICLR | Year-specific class |
+| `aaai24` / `aaai25` | AAAI | Year-specific class |
+| `IEEEtran` | IEEE conferences | `conference` option |
+| `article` | Generic | Various options |
+
+Also detect relevant options:
+- `anonymous` -- anonymous submission mode
+- `review` -- review/submission mode
+- `nonacm` -- non-ACM affiliated (used in KDD)
+- `sigconf` -- ACM SIGCONF format
+
+### Step 1.5: Diagnose Issues
+
+Check the template for common problems that need cleanup:
+
+**Disorganized file structure**:
+- Multi-level directory nesting where flat would suffice
+- .tex files scattered across multiple directories
+- Images mixed with source files
+
+**Redundant content**:
+- Files named `sample*`, `example*`, `demo*`, `test*`
+- Multiple versions of the same file
+- Template documentation files (e.g., `acmguide.pdf`)
+
+**Excessive comments**:
+- Instructional comments like `%% DELETE THIS SECTION`
+- Long blocks of commented-out example text
+- Tutorial-style inline comments explaining LaTeX basics
+
+**Missing dependencies**:
+- .sty or .cls files referenced in `\usepackage` or `\documentclass` but not present in the archive
+- Check `\RequirePackage` statements in .cls files
+
+**Incorrect reference paths**:
+- `\includegraphics` paths that reference non-existent locations
+- `\input` or `\include` paths that would break after reorganization
+- `\bibliography` path mismatches
+
+```bash
+# Check for redundant files
+echo "=== Potential Redundant Files ==="
+find "$TEMP_DIR" -type f \( -name "sample*" -o -name "example*" -o -name "demo*" -o -name "test*" \) | grep -i '\.tex$'
+
+# Check for excessive comments (instructional markers)
+echo "=== Instructional Comment Markers ==="
+grep -rn 'DELETE\|REMOVE\|TODO.*delete\|Replace this\|Your .* here' "$TEMP_DIR" --include="*.tex" | head -20
+
+# Check referenced packages
+echo "=== Referenced Packages ==="
+grep -rh '\\usepackage' "$MAIN_FILE" | sed 's/.*{\(.*\)}.*/\1/' | sort -u
+
+# Check image references
+echo "=== Image References ==="
+grep -rh '\\includegraphics' "$MAIN_FILE" | head -20
+```
+
+### Step 1.6: Present Analysis
+
+Present the complete analysis to the user in a structured format:
+
+```
+=== Template Analysis ===
+
+1. File Inventory:
+   - LaTeX sources: N files
+   - Style files: N files (.sty/.cls/.bst)
+   - Bibliography: N files
+   - Images: N files
+   - Other: N files
+   - Total: N files
+
+2. Main File: [filename]
+   - Document class: [class] with options [options]
+
+3. Conference: [detected conference name]
+   - Type: [submission/camera-ready]
+   - Anonymous: [yes/no]
+
+4. Issues Found:
+   - [x] Disorganized structure: [details]
+   - [x] Redundant files: [list]
+   - [x] Excessive comments: [count] instructional markers
+   - [ ] Missing dependencies: none
+   - [x] Path issues: [details]
+
+5. Proposed Cleanup Plan:
+   a. Create clean directory structure (main.tex, text/, figures/, tables/, styles/)
+   b. Extract and clean main.tex (remove examples, keep config)
+   c. Create section files in text/
+   d. Copy style files to styles/
+   e. Copy images to figures/
+   f. Consolidate bibliography to references.bib
+   g. Remove [N] redundant files
+
+Proceed with cleanup? (Y/n)
+```
+
+Wait for user confirmation before proceeding to Phase 2.
+
+## Output
+
+`analysisResult` object containing:
+
+| Field | Type | Description |
+|-------|------|-------------|
+| `fileInventory` | object | Categorized file lists (tex, sty, bib, images, other) |
+| `mainFile` | string | Path to identified main .tex file |
+| `conferenceType` | object | `{class, options, conference, anonymous}` |
+| `issues` | array | List of diagnosed issues with severity |
+| `approvedPlan` | boolean | Whether user approved the cleanup plan |
+| `tempDir` | string | Path to temporary extraction directory |
+
+## Next Phase
+
+Phase 2: Cleanup & Organize (`phases/02-cleanup-organize.md`)
+- Receives: `analysisResult`, `sectionStructure`, `outputDir`
+- Creates the clean directory structure and reorganizes files