Version 2 Refactoring: Restructure Repository with Experimental and Legacy Submodules

[Sinitca-Aleksandr]

This issue tracks the comprehensive refactoring of the repository structure for Version 2. The key objectives are:

1. Rename the root module to fluctuation_analysis_tools for better clarity
2. Introduce an experimental submodule for new features under development
3. Create a legacy submodule ensuring backward compatibility with v1.*

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Proposed Changes

Repository Structure

fluctuation-analysis-tools/
├── fluctuation_analysis_tools/          # Root module (renamed)
│   ├── analysis/                       # Core analysis functions
│   ├── generators/                     # Data generation tools
│   ├── filters/                        # Filtering utilities
│   ├── visualization/                  # Visualization tools
│   ├── auxiliary/                      # Helper functions
│   ├── experimental/                   # New features (unstable)
│   └── legacy/                         # v1.* compatibility layer
├── setup.py
└── pyproject.toml

Key Features

• Experimental Submodule: Isolated workspace for new features with clear opt-in usage
• Legacy Submodule: Maintains v1.* API via from fluctuation_analysis_tools.legacy import StatTools
• Improved Organization: Logical grouping of related functionality

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Implementation Plan

1. Rename root module from StatTools to fluctuation_analysis_tools
2. Restructure code into logical submodules
3. Create legacy compatibility layer
4. Update all documentation and configuration files
5. Comprehensive testing of migration path

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Testing Requirements

• Verify backward compatibility through legacy submodule
• Test experimental features in isolation
• Confirm all existing functionality remains intact