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docs: Update documentation for unified directory structure (#52)

* docs: Update documentation for unified directory structure

- Update README.md references from 'teddy_reference_outputs' to 'reference_output'
- Expand project structure documentation to include all unified directories
- Update reference_output/index.md to reflect unified BDD analysis structure
- Remove CUDD-specific vs TeDDy-specific references in favor of cross-library validation approach
- Add Python integration references and edge case documentation
- Clean up directory structure by removing empty teddy_expected_output subdirectory

All documentation now properly reflects the unified test_expressions/ structure:
- expected_output/ (unified reference files)
- reference_output/ (analysis documentation)
- edge_cases/ (edge case files and analysis)
- reordered/ and default_ordering/ (variable ordering tests)

Signed-off-by: Alan Jowett <alan.jowett@microsoft.com>

* docs: Update CUDD canonicality references to reflect resolved status

- Remove references to CUDD canonicality 'issues' and 'problems'
- Update Python BDD documentation to focus on cross-library validation
- Change examples to show all implementations producing canonical output
- Update docstrings and integration guides to reflect current capabilities
- Replace 'issue detection' language with 'cross-validation' terminology

All BDD implementations (TeDDy, CUDD, Python) now produce canonical output.
Documentation updated to reflect this current state rather than historical issues.

Signed-off-by: Alan Jowett <alan.jowett@microsoft.com>

* docs: Add SPDX license headers and improve Doxygen documentation

- Add SPDX-License-Identifier: MIT headers to all source files missing them
- Add comprehensive Doxygen file-level documentation to C++ header files
- Improve function-level documentation for key iterator classes
- Add SPDX headers to Python, shell, and CMake files
- Document key functions in teddy_iterator with @brief and @... (continued)

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