Migrate command-line tools from CommandLineParser to System.CommandLine

[Copilot]

This PR migrates all command-line tools in the repository from the third-party CommandLineParser library to Microsoft's official System.CommandLine library (currently in preview), as requested in the issue.

Changes Made

Package Updates

• FHIR Tools: Updated both R4 and Stu3 CommandLineTool projects to use System.CommandLine v2.0.0-beta4.22272.1
• DICOM Tool: Updated CommandLineTool project to use System.CommandLine v2.0.0-beta4.22272.1
• Removed all references to CommandLineParser (versions 2.8.0-2.9.1)

Code Migration

• FHIR Shared Code: Completely rewrote Microsoft.Health.Fhir.Anonymizer.Shared.CommandLineTool/Program.cs to use System.CommandLine's modern API with proper option definitions and handlers
• DICOM Tool: Migrated AnonymizerCliTool.cs and simplified AnonymizerOptions.cs to work with System.CommandLine's approach
• Command-Line Interface: Maintained full backward compatibility - all existing options and behaviors preserved

Enhanced Features

• Better Help Output: System.CommandLine provides cleaner, more consistent help formatting
• Improved Error Handling: Enhanced validation and error messages using System.CommandLine's built-in features
• Modern API: Leverages System.CommandLine's contemporary parsing patterns and type safety

Validation

All command-line tools have been thoroughly tested:

• FHIR R4 Anonymizer: Successfully processed 13 sample FHIR R4 files
• FHIR Stu3 Anonymizer: Successfully processed 11 sample FHIR Stu3 files
• DICOM Anonymizer: Successfully processed sample DICOM files in both single-file and folder modes
• Unit Tests: All existing DICOM command-line unit tests continue to pass (12/12)
• Help Output: Verified clean help formatting for all tools

Example Usage

The command-line interface remains unchanged for users:

# FHIR R4 (unchanged)
./Microsoft.Health.Fhir.Anonymizer.R4.CommandLineTool -i input_folder -o output_folder -v

# DICOM (unchanged) 
./Microsoft.Health.Dicom.Anonymizer.CommandLineTool -I input_folder -O output_folder

But now with improved help output:

Usage:
  Microsoft.Health.Fhir.Anonymizer.R4.CommandLineTool [options]

Options:
  -i, --inputFolder <inputFolder> (REQUIRED)    Folder to locate input resource files.
  -o, --outputFolder <outputFolder> (REQUIRED)  Folder to save anonymized resource files.
  -v, --verbose                                 Provide additional details in processing.
  --help                                        Show help and usage information

This migration positions the project to use Microsoft's official command-line parsing library while maintaining full compatibility with existing usage patterns.

Fixes #255.

---

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.