[FEATURE] Implement hierarchical configuration system with enhanced error handling

[dwenzel]

Summary

• Implement hierarchical configuration system with precedence levels for flexible project configuration
• Add ConfigurationDiscovery for automatic file detection across project hierarchies
• Implement ConfigurationMerger for intelligent array/object merging with type preservation
• Replace error_log with proper console error reporting architecture
• Fix dependency injection issues affecting configuration commands
• Remove obsolete config/quality-tools.yaml (replaced by built-in defaults)

Changes

• New Configuration System: HierarchicalConfigurationLoader with discovery and merging
• Enhanced Error Handling: Proper console error reporting instead of error_log
• Dependency Injection Fixes: Exclude classes requiring runtime parameters from autowiring
• Array Merging: Fix indexing preservation during configuration merge operations
• Documentation: Complete configuration reference with precedence hierarchy
• Architecture: Improved separation between production and test error handling

Test Results

All 706 tests pass with clean output - no error log clutter in PHPUnit CLI

Closes

Closes #1

🤖 Generated with Claude Code

[vladimirfalconpiva]

@dwenzel

File Configuration override did not work for me in ZUG System

zug-bundle-13 git:(feature/rector-AsEventListener-Attribute)

Test:

• Tested with a rector.php file in project root
• Tested with a rector.php file in config folder

Executed ddev composer lint:rector Local file configuration in both location is ignored.

ddev exec ./app/vendor/bin/qt config:show

Trows:

vfalcon@zug-13-web:/var/www/html$ ./app/vendor/bin/qt config:show

                                                                                                                        
 [ERROR] Failed to load configuration:                                                                                  
                                                                                                                        
         Configuration file error [merged]: Invalid merged configuration:                                               
         : The property tool_config_file is not defined and the definition does not allow additional properties         
         : The property custom_config is not defined and the definition does not allow additional properties 

[dwenzel]

@vladimirfalconpiva Thank you for testing and reporting this issue!

Your observation is absolutely correct. The configuration file override functionality is broken due to a schema validation conflict. The system discovers custom tool configs (like rector.php) but adds runtime metadata keys (tool_config_file, custom_config) that aren't defined in our JSON schema, causing validation failures.

Where we'll fix it: We've documented this as Issue 022 and plan to resolve it through a config_file key approach in the user YAML schema, eliminating the schema validation conflicts while providing explicit user control.

Why as a side quest: Since this issue affects the configuration system we're refactoring in 019, we decided to address it properly rather than applying a quick fix that might conflict with the new architecture. This ensures a clean, maintainable solution.

The fix will take some time to implement properly with comprehensive testing. Work is tracked in the issue-022-configuration-file-replacement-fix branch. Thanks for helping us catch this early in the refactoring process!