diff --git a/PRD.md b/PRD.md
index 4934a4a..d233539 100644
--- a/PRD.md
+++ b/PRD.md
@@ -48,16 +48,26 @@ These principles are fundamental to the project's long-term success and must be
 
 - **PRD.md Updates:** Any changes to project requirements, architecture, or functionality must be reflected in this document
 - **README.md Updates:** User-facing features, installation instructions, or usage changes must be documented
+- **CLI Commands Documentation:** All CLI functionality, options, and usage examples must be documented in `cli/commands.txt`
 - **Code Comments:** Significant logic changes should include inline documentation
 - **API Documentation:** New endpoints, functions, or interfaces must be documented
 
 **Documentation Update Checklist:**
 - [ ] Update PRD.md with any architectural or requirement changes
 - [ ] Update README.md with new features, installation steps, or usage instructions
+- [ ] Update `cli/commands.txt` with any new CLI options, examples, or functionality changes
 - [ ] Add inline comments for complex logic or business rules
 - [ ] Update any configuration examples or file structure documentation
 - [ ] Review and update implementation status sections
 
+**CLI Commands Documentation Requirements:**
+- **Comprehensive Coverage:** All CLI arguments, options, and flags must be documented with examples
+- **Usage Examples:** Provide practical examples for common use cases and combinations
+- **Configuration Details:** Document all configuration options and their effects
+- **Error Handling:** Include troubleshooting information and common issues
+- **Integration Notes:** Document how CLI integrates with web UI and other components
+- **Version Tracking:** Keep version information and feature status up to date
+
 This documentation requirement is mandatory and ensures the project remains maintainable and accessible to future developers and users.
 
 ### 2.3 Code Quality & Development Standards
@@ -230,7 +240,8 @@ KaraokeMerge/
 │   ├── matching.py            # Song matching logic
 │   ├── report.py              # Report generation
 │   ├── preferences.py         # Priority preferences management
-│   └── utils.py               # Utility functions
+│   ├── utils.py               # Utility functions
+│   └── commands.txt           # Comprehensive CLI commands reference
 ├── web/                       # Web UI for manual review
 │   ├── app.py                 # Flask web application
 │   └── templates/
diff --git a/cli/__pycache__/matching.cpython-313.pyc b/cli/__pycache__/matching.cpython-313.pyc
index 288c541..314acf2 100644
Binary files a/cli/__pycache__/matching.cpython-313.pyc and b/cli/__pycache__/matching.cpython-313.pyc differ
diff --git a/cli/commands.txt b/cli/commands.txt
new file mode 100644
index 0000000..b534e44
--- /dev/null
+++ b/cli/commands.txt
@@ -0,0 +1,262 @@
+# Karaoke Song Library Cleanup Tool - CLI Commands Reference
+
+## Overview
+The CLI tool analyzes karaoke song collections, identifies duplicates, and generates skip lists for future imports. It supports multiple file formats (MP3, CDG, MP4) with configurable priority systems.
+
+## Basic Usage
+
+### Standard Analysis
+```bash
+python cli/main.py
+```
+Runs the tool with default settings:
+- Input: `data/allSongs.json`
+- Config: `config/config.json`
+- Output: `data/skipSongs.json`
+- Verbose: Disabled
+- Reports: Not saved
+
+### Verbose Output
+```bash
+python cli/main.py --verbose
+# or
+python cli/main.py -v
+```
+Enables detailed output showing:
+- Individual song processing
+- Duplicate detection details
+- File type analysis
+- Channel priority decisions
+
+### Dry Run Mode
+```bash
+python cli/main.py --dry-run
+```
+Analyzes songs without generating the skip list file. Useful for:
+- Testing configuration changes
+- Previewing results before committing
+- Validating input data
+
+## Configuration Options
+
+### Custom Configuration File
+```bash
+python cli/main.py --config path/to/custom_config.json
+```
+Uses a custom configuration file instead of the default `config/config.json`.
+
+### Show Current Configuration
+```bash
+python cli/main.py --show-config
+```
+Displays the current configuration settings and exits. Useful for:
+- Verifying configuration values
+- Debugging configuration issues
+- Understanding current settings
+
+## Input/Output Options
+
+### Custom Input File
+```bash
+python cli/main.py --input path/to/songs.json
+```
+Specifies a custom input file instead of the default `data/allSongs.json`.
+
+### Custom Output Directory
+```bash
+python cli/main.py --output-dir ./custom_output
+```
+Saves output files to a custom directory instead of the default `data/` folder.
+
+## Report Generation
+
+### Save Detailed Reports
+```bash
+python cli/main.py --save-reports
+```
+Generates comprehensive analysis reports in the output directory:
+- `enhanced_summary_report.txt` - Comprehensive analysis
+- `channel_optimization_report.txt` - Priority optimization suggestions
+- `duplicate_pattern_report.txt` - Duplicate pattern analysis
+- `actionable_insights_report.txt` - Recommendations and insights
+- `detailed_duplicate_analysis.txt` - Specific songs and their duplicates
+- `analysis_data.json` - Raw analysis data for further processing
+- `skip_songs_detailed.json` - Full skip list with metadata
+
+## Combined Examples
+
+### Full Analysis with Reports
+```bash
+python cli/main.py --verbose --save-reports
+```
+Runs complete analysis with:
+- Verbose output for detailed processing information
+- Comprehensive report generation
+- Skip list creation
+
+### Custom Configuration with Dry Run
+```bash
+python cli/main.py --config custom_config.json --dry-run --verbose
+```
+Tests a custom configuration without generating files:
+- Uses custom configuration
+- Shows detailed processing
+- No output files created
+
+### Custom Input/Output with Reports
+```bash
+python cli/main.py --input /path/to/songs.json --output-dir ./reports --save-reports
+```
+Processes custom input and saves all outputs to reports directory:
+- Custom input file
+- Custom output location
+- All report files generated
+
+### Minimal Output
+```bash
+python cli/main.py --output-dir ./minimal
+```
+Runs with minimal output:
+- No verbose logging
+- No detailed reports
+- Only generates skip list
+
+## Configuration File Structure
+
+The default configuration file (`config/config.json`) contains:
+
+```json
+{
+  "channel_priorities": [
+    "Sing King Karaoke",
+    "KaraFun Karaoke", 
+    "Stingray Karaoke"
+  ],
+  "matching": {
+    "fuzzy_matching": false,
+    "fuzzy_threshold": 0.85,
+    "case_sensitive": false
+  },
+  "output": {
+    "verbose": false,
+    "include_reasons": true,
+    "max_duplicates_per_song": 10
+  },
+  "file_types": {
+    "supported_extensions": [".mp3", ".cdg", ".mp4"],
+    "mp4_extensions": [".mp4"]
+  }
+}
+```
+
+### Configuration Options Explained
+
+#### Channel Priorities
+- **channel_priorities**: Array of folder names for MP4 files
+- Order determines priority (first = highest priority)
+- Files without matching folders are marked for manual review
+
+#### Matching Settings
+- **fuzzy_matching**: Enable/disable fuzzy string matching
+- **fuzzy_threshold**: Similarity threshold (0.0-1.0) for fuzzy matching
+- **case_sensitive**: Case-sensitive artist/title comparison
+
+#### Output Settings
+- **verbose**: Enable detailed output
+- **include_reasons**: Include reason field in skip list
+- **max_duplicates_per_song**: Maximum duplicates to process per song
+
+#### File Type Settings
+- **supported_extensions**: All supported file extensions
+- **mp4_extensions**: Extensions treated as MP4 files
+
+## Input File Format
+
+The tool expects a JSON array of song objects:
+
+```json
+[
+  {
+    "artist": "Artist Name",
+    "title": "Song Title", 
+    "path": "path/to/file.mp3"
+  }
+]
+```
+
+Optional fields for MP4 files:
+- `channel`: Channel/folder information
+- ID3 tag information (artist, title, etc.)
+
+## Output Files
+
+### Primary Output
+- **skipSongs.json**: List of file paths to skip in future imports
+- Format: `[{"path": "file/path.mp3", "reason": "duplicate"}]`
+
+### Report Files (with --save-reports)
+- **enhanced_summary_report.txt**: Overall analysis and statistics
+- **channel_optimization_report.txt**: Channel priority suggestions
+- **duplicate_pattern_report.txt**: Duplicate detection patterns
+- **actionable_insights_report.txt**: Recommendations for collection management
+- **detailed_duplicate_analysis.txt**: Specific duplicate groups
+- **analysis_data.json**: Raw data for further processing
+- **skip_songs_detailed.json**: Complete skip list with metadata
+
+## File Type Priority System
+
+The tool processes files in this priority order:
+
+1. **MP4 files** (with channel priority sorting)
+2. **CDG/MP3 pairs** (treated as single units)
+3. **Standalone MP3** files
+4. **Standalone CDG** files
+
+## Error Handling
+
+The tool provides clear error messages for:
+- Missing input files
+- Invalid JSON format
+- Configuration errors
+- File permission issues
+- Processing errors
+
+## Performance Notes
+
+- Successfully tested with 37,000+ songs
+- Processes large datasets efficiently
+- Shows progress indicators for long operations
+- Memory-efficient processing
+
+## Integration with Web UI
+
+The CLI tool integrates with the web UI:
+- Web UI can load CLI-generated data
+- Priority preferences from web UI are used by CLI
+- Shared configuration and data files
+- Consistent processing logic
+
+## Troubleshooting
+
+### Common Issues
+1. **File not found**: Check input file path and permissions
+2. **JSON errors**: Validate input file format
+3. **Configuration errors**: Use --show-config to verify settings
+4. **Permission errors**: Check output directory permissions
+
+### Debug Mode
+```bash
+python cli/main.py --verbose --dry-run --show-config
+```
+Complete debugging setup:
+- Shows configuration
+- Verbose processing
+- No file changes
+
+## Version Information
+
+This commands reference is for Karaoke Song Library Cleanup Tool v2.0
+- CLI: Fully functional with comprehensive options
+- Web UI: Interactive priority management
+- Priority System: Drag-and-drop with persistence
+- Reports: Enhanced analysis with actionable insights 
\ No newline at end of file
diff --git a/cli/main.py b/cli/main.py
index 491858c..c3c2933 100644
--- a/cli/main.py
+++ b/cli/main.py
@@ -123,6 +123,7 @@ def main():
     songs = load_songs(args.input)
     
     # Initialize components
+    data_dir = args.output_dir
     matcher = SongMatcher(config, data_dir)
     reporter = ReportGenerator(config)