docs: clarify licensing terms for third-party foundation models

- Update README.md and LICENSE to explicitly state that commercial
  agreements cover only the SpatialTranscriptFormer source code and IP.
- Add a disclaimer clarify that rights for restricted foundation model
  weights (e.g., CTransPath, Phikon) must be obtained separately.
- Recommend Apache 2.0 alternatives (Hibou, Virchow, H-Optimus-0)
  for commercial use cases to avoid licensing conflicts.

Author: BenjaminIsaac0111

LICENSE

@@ -11,6 +11,8 @@ This software and its source code are provided for the following purposes:
 2. COMMERCIAL USE (NEGOTIATED AGREEMENT REQUIRED)
 Use of this software, its source code, or derivative works by for-profit entities, or for any commercial or revenue-generating purposes, is strictly prohibited without a separate, written license agreement negotiated with and signed by the Author.
 
+Foundation Model Disclaimer: This software is designed to be backbone-agnostic and relies on third-party foundation models for feature extraction. A commercial agreement with the Author covers ONLY the SpatialTranscriptFormer source code, architecture, and intellectual property. It DOES NOT grant commercial use rights for restricted third-party models (e.g., CTransPath or Phikon). To use this software commercially, you must pair it with a backbone model that has a compatible commercial-friendly license (e.g., Apache 2.0 models like Hibou, Virchow, or H-Optimus-0).
+
 Interested parties should contact the Author directly to discuss commercial licensing terms.
 
 1. ATTRIBUTION

README.md

@@ -19,6 +19,7 @@ This project is protected by a **Proprietary Source Code License**. See the [LIC
 
 - ✅ **Permitted**: Evaluation for employment, Academic Research, and Non-Profit use.
 - 🤝 **For-Profit Use**: Permitted only under a **negotiated agreement** with the author.
+  - **Note on Foundation Models**: This architecture is backbone-agnostic. Any negotiated commercial agreement covers *only* the SpatialTranscriptFormer source code and IP. It does **not** grant commercial rights to use restricted third-party weights (e.g., CTransPath, Phikon). To use this system commercially, you must select a foundation model with a compatible open or commercial license (e.g., Hibou, Virchow, or H-Optimus-0).
 - ❌ **Prohibited**: Redistribution and unauthorized commercial exploitation.
 
 ## Intellectual Property