Refactor entrypoints and initialization throughout

[BeckettFrey]

This pull request modernizes and clarifies the VoxKit codebase by improving logging, updating module and API documentation, and refactoring naming for consistency. The most important changes include switching from print statements to structured logging, renaming the main GUI class for clarity, and updating module docstrings and API lists to better reflect the current structure and functionality.

Logging and Environment Setup:

• Replaced all print statements in main.py with structured logging using a named logger, and added early logging configuration so log messages are properly captured even before the main logger setup. [1] [2] [3]
• Added logging configuration and log handler utilities to the config module, making log setup and access more modular. [1] [2] [3] [4]

Naming and API Consistency:

• Renamed the main GUI class from AlignmentGUI to VoxKitGUI throughout the codebase for clarity and future extensibility. Updated all references and API exports accordingly. [1] [2] [3] [4] [5]
• Updated the __all__ exports in several modules to only expose the intended public interfaces, removing unnecessary or outdated exports. [1] [2] [3]

Module Documentation and API Lists:

• Revised and clarified module-level docstrings in __init__.py files across the codebase, providing accurate descriptions of submodules, APIs, and available engines/analyzers. [1] [2] [3] [4] [5] [6] [7] [8] [9]
• Simplified or shortened docstrings in GUI component modules for conciseness and to reduce redundancy. [1] [2] [3] [4] [5] [6] [7]

Versioning and Metadata:

• Updated the package version and author metadata in src/voxkit/__init__.py to reflect the current release and contact information.

Other Minor Refactors:

• Removed unused imports and legacy comments, and improved comments for clarity, especially regarding the frozen app environment and multiprocessing. [1] [2]

These changes collectively improve maintainability, user experience, and developer clarity across the VoxKit project.