Fixes and updates with some new features.

[unixwzrd]

Core Library Enhancements

• Enhanced variable handling with new update_variable function

• Improved configuration management with better validation

• Enhanced error handling and logging

• Added support for configuration inheritance

• Setup and Installation

• Added new refresh option for updating from cloned repos

• Fixed bashrc modification issues

• Improved configuration handling

• Enhanced error reporting

• File Management

• Improved pattern processing in filetree.py

• Enhanced configuration file handling

• Better handling of empty patterns

• Added support for both file extensions and patterns

• Documentation

• Removed redundant debug level documentation

• Enhanced help messages and usage documentation

• Improved error messages and logging

• Updated configuration documentation

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