cli warning added

Author: prathameshnium

README.md

@@ -178,6 +178,8 @@ PICA is structured as a standard Python package.
     ```bash
     pica-cli
     ```
+    > [!WARNING]
+    > **CLI Deprecation Notice:** The PICA CLI is comprised of old, deprecated scripts from the early stages of development. It is **strongly recommended to use the PICA GUI** for all interactions. The CLI scripts are considered legacy code, contain minimal functionality for performing set protocols, and are not recommended for general use.
 
 ---
 ## Running Tests

docs/User_Manual.md

@@ -113,6 +113,8 @@ Launch the main dashboard:
 ```bash
 python run_pica.py
 ```
+> [!WARNING]
+> **CLI Deprecation Notice:** The PICA CLI is comprised of old, deprecated scripts from the early stages of development. It is **strongly recommended to use the PICA GUI** for all interactions. The CLI scripts are considered legacy code, contain minimal functionality for performing set protocols, and are not recommended for general use.
 
 ### 3.4 Development Dependencies (Optional)