feat: Add custom dependency file support with proper path resolution

Implements comprehensive per-repository custom dependency file paths and names
with dependency isolation and correct relative path resolution.

## New Features

### Custom Dependency File Configuration
- Add "Dependency File Path" field for custom subdirectories
- Add "Dependency File Name" field for custom file names
- Support both fields independently or together
- Maintain full backward compatibility

### Dependency Isolation
- Custom settings apply only to defining repository
- Nested repositories use default dependency file names
- Prevents configuration coupling between parent/child repos
- Maintains clean separation of concerns

### Fixed Path Resolution
- Relative paths now correctly resolve from repository root
- Fixed critical bug where paths resolved from dependency file location
- Proper handling of ".." segments in nested structures
- Intuitive behavior matching user expectations

## Technical Implementation

### Core Changes
- Enhanced `Get-AbsoluteBasePath()` with repository root context
- Added `Get-CustomDependencyFilePath()` for custom file resolution
- Updated function signatures throughout call chain
- Extended repository dictionary for custom settings storage

### Path Resolution Flow
- Root dependencies: Relative to dependency file directory
- Nested dependencies: Relative to repository root directory
- Repository root path passed through processing chain
- Proper normalization of all path types

### Quality Assurance
- Extensive testing of partial API overlap scenarios
- Validated incompatible API handling
- Tested custom path and filename configurations
- Verified correct relative path resolution
- Confirmed dependency isolation behavior

## Configuration Examples

### Basic Custom Name
```json
{
  "Repository URL": "https://github.com/org/repo.git",
  "Base Path": "repos/project",
  "Tag": "v1.0.0",
  "Dependency File Name": "project-modules.json"
}
```

### Custom Path and Name
```json
{
  "Repository URL": "https://github.com/org/repo.git",
  "Base Path": "repos/project",
  "Tag": "v1.0.0",
  "Dependency File Path": "config/deps",
  "Dependency File Name": "external-deps.json"
}
```

### Path Resolution Example
```
Repository: project/
Custom file: project/build/config/deps.json
Relative path: ../libs/shared
Resolves to: project/libs/shared (✅ repo root)
Not: project/build/libs/shared (❌ file location)
```

## Benefits

### For Organizations
- Support diverse project structures and naming conventions
- Enable gradual migration from existing systems
- Accommodate team-specific preferences
- Maintain configuration boundaries

### For Developers
- Intuitive relative path behavior
- Flexible dependency file organization
- Clear separation between repositories
- Enhanced debugging capabilities

### For Enterprise
- Compliance with organizational standards
- Integration with existing tooling
- Scalable multi-team support
- Robust error handling

## Documentation Updates
- Comprehensive README section on custom dependency files
- Updated CHANGELOG with detailed feature description
- New example configuration files
- Enhanced troubleshooting guide

## Backward Compatibility
- Zero breaking changes
- All existing configurations work unchanged
- Optional feature with sensible defaults
- Seamless upgrade path from v6.0.x

Closes #5

Co-authored-by: Claude (Anthropic) <claude@anthropic.com>

Author: AndreaV-Lsi

CHANGELOG.md

@@ -5,6 +5,85 @@ All notable changes to LsiGitCheckout will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [6.1.0] - 2025-01-24
+
+### Added
+- **Custom Dependency File Support**: Added support for per-repository custom dependency file paths and names via "Dependency File Path" and "Dependency File Name" fields
+- **Repository-Level Dependency Configuration**: Each repository can specify its own dependency file location without affecting nested repositories
+- **Proper Path Resolution**: Relative paths in dependency files are now correctly resolved from repository root directories, not dependency file locations
+- **Isolation of Custom Settings**: Custom dependency file settings are not propagated to nested repositories (preserves dependency isolation)
+- Enhanced logging for custom dependency file configurations showing when custom paths/names are used
+- New `Get-CustomDependencyFilePath` function for resolving custom dependency file locations with proper path resolution
+- Summary statistics showing count of repositories using custom dependency file configurations
+
+### Changed
+- **Repository Dictionary Enhancement**: Extended repository dictionary to track custom dependency file settings per repository
+- **Recursive Processing Improvement**: Modified recursive dependency processing to handle per-repository custom dependency files while maintaining isolation
+- **Path Resolution Fix**: Fixed critical issue where relative paths were incorrectly resolved from dependency file directories instead of repository roots
+- Enhanced verbose logging to show custom dependency file path and name configurations during repository processing
+- Improved dependency file resolution logic to support both relative and absolute custom paths with correct base path calculation
+- Updated function signatures to support repository root path context for proper relative path resolution
+
+### Fixed
+- **Critical Path Resolution Bug**: Relative paths in nested dependency files now correctly resolve from the repository root instead of the dependency file's directory location
+- Resolved issue where custom dependency file paths could create incorrect absolute paths leading to repository conflicts
+- Fixed path calculation logic to properly handle ".." segments relative to repository roots
+
+### Benefits
+- **Flexible Dependency Management**: Repositories can use different dependency file naming conventions (e.g., "project-deps.json", "modules.json")
+- **Custom Directory Structure Support**: Dependency files can be located in subdirectories (e.g., "config/deps", "build/dependencies")
+- **Correct Path Behavior**: Relative paths in dependency files work as users expect (relative to repository root)
+- **Backward Compatibility**: All existing repositories continue to work without modification
+- **Dependency Isolation**: Custom settings don't leak to nested repositories, preventing unintended dependency file lookups
+- **Mixed Convention Support**: Teams can mix different dependency file conventions within the same project hierarchy
+- **Robust Path Resolution**: Eliminates path conflicts caused by incorrect relative path calculation
+
+### Configuration Examples
+
+#### Repository with Custom Dependency File Path and Name
+```json
+{
+  "Repository URL": "https://github.com/myorg/project.git",
+  "Base Path": "repos/project",
+  "Tag": "v1.0.0",
+  "Dependency File Path": "config/deps",
+  "Dependency File Name": "project-dependencies.json"
+}
+```
+
+#### Repository with Custom File Name Only
+```json
+{
+  "Repository URL": "https://github.com/myorg/library.git",
+  "Base Path": "libs/library",
+  "Tag": "v2.0.0",
+  "Dependency File Name": "modules.json"
+}
+```
+
+#### Correct Path Resolution Example
+```
+Repository root: /project/
+Custom dependency file: /project/build/config/deps.json
+Relative path in deps.json: ../libs/shared
+Correctly resolves to: /project/libs/shared (relative to repository root)
+```
+
+### Technical Implementation
+- Custom dependency file settings are stored in the repository dictionary but not propagated during recursive processing
+- Nested repositories always use the default dependency file name from the root invocation
+- Path resolution supports both relative paths (relative to repository root) and subdirectories
+- Enhanced `Get-AbsoluteBasePath` function with repository root context parameter
+- Updated `Process-DependencyFile`, `Invoke-GitCheckout`, and `Update-RepositoryDictionary` functions to support repository root path context
+- Maintains full backward compatibility with existing dependency file conventions
+
+### Migration Notes
+- **Zero configuration changes required**: All existing repositories work without modification
+- **Optional feature**: Custom dependency file settings are completely optional
+- **Gradual adoption**: Teams can add custom settings to repositories as needed
+- **Path resolution improvement**: Existing relative paths now work more intuitively
+- **Enhanced debugging**: Better logging for troubleshooting path resolution issues
+
 ## [6.0.0] - 2025-01-24
 
 ### Breaking Changes