Add UTF-8 encoding support for Windows console in run.py and logger.py to prevent character encoding issues

Remove startup message logging from the Flask application in `run.py` to streamline output during server initialization. This change simplifies the code and reduces unnecessary console output, particularly in debug mode.

Remove warnings suppression for multiprocessing in run scripts

Enhance signal handling and suppress warnings in simulation scripts

Enhance backend startup logging and API endpoint display

Introduce Project ID for context management, finalizing the stateful API pipeline from file submission to graph construction.