Scientific Consistency and Framework Restructuring

[divyang4481]

This PR implements a comprehensive update to the X-Theta framework to ensure scientific discipline and notation consistency.

Key changes:

1. Notation Standardization: Throughout the xtheta/ package, tests/, and notebooks, we now strictly use Phi (capital) for the physical relational phase/holonomy and delta (lowercase) for phenomenological detector phase shifts.
2. Formula Correction: Ensured that the physical X-Theta CHSH maximum uses the basis-optimized Horodecki formula $S_{\max}(\Phi) = 2\sqrt{1 + \cos^2(2\Phi)}$.
3. Notebook Restructuring:
   • Renumbered notebooks to a clean 01-08 sequence.
   • Merged the two Hensen data audit notebooks into a single canonical 06_hensen_open_data_audit.ipynb.
   • Updated 07_synthetic_phase_recovery.ipynb to include two distinct models: Model A (detector shift using delta) and Model B (physical tensor anisotropy using Phi).
4. Scientific Framing:
   • Added 'Scientific Scope' warning blocks to the top of all relevant notebooks.
   • Updated notebook conclusions to explicitly classify results into Mathematical Validation, Simulation/Benchmark, Open-Data Pipeline Validation, Phenomenological Fit, or Physical Prediction.
   • Explicitly framed Earth-orbit (Micius/GPS) benchmarks as null-regime consistency checks and Hensen audits as pipeline validation only.
5. Documentation: Updated the paper_1_kinematic_framework/outline.md to reflect the new 9-section structure and included a notebook traceability table.
6. Code Maintenance: Renamed internal files and updated imports (e.g., phi_eff_fit.py -> Phi_eff_fit.py) to align with the new notation.

All 47 unit tests passed after these widespread changes.

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PR created automatically by Jules for task 9364016472972784613 started by @divyang4481

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