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Based on your requirements and the suggestions provided, here is the updated Python script for setting up a Telegram chatbot using the `python-telegram-bot` library, refactored to adhere to best practices:

```python
import os
import logging
from telegram import Update
from telegram.ext import Application, CommandHandler, MessageHandler, ContextTypes, filters
from dotenv import load_dotenv

# Load environment variables from a .env file
load_dotenv()
telegram_api_token = os.getenv('TELEGRAM_API_TOKEN')

# Setup logging
logging.basicConfig(
    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
    level=logging.INFO
)

# Dictionary to keep track of user histories
user_histories = {}

async def start(update: Update, context: ContextTypes.DEFAULT_TYPE) -> None:
    """
    Handles the /start command. Initiates a conversation with the user.
    """
    await update.message.reply_text('Hello! I am your chatbot. Start talking to me!')

async def clear_history(update: Update, context: ContextTypes.DEFAULT_TYPE) -> None:
    """
    Clears the chat history for the user who issued the /clear command.
    """
    user_id = update.message.from_user.id
    user_histories.pop(user_id, None)
    await update.message.reply_text('Your history has been cleared!')

async def chat(update: Update, context: ContextTypes.DEFAULT_TYPE):
    """
    Handles incoming messages and generates responses.
    """
    try:
        user_id = update.message.from_user.id
        user_message = update.message.text
        history = user_histories.setdefault(user_id, [])
        sys_prompt = "Your system prompt here"

        # Replace this with the actual model client implementation
        response = model_client.get_response(user_message, history, sys_prompt) 

        history.append((user_message, response))
        await update.message.reply_text(response)
    except Exception as e:
        await update.message.reply_text("An error occurred. Please try again.")
        logging.error(f"Error in chat handler: {e}")

async def main():
    """
    Initializes the Telegram bot application.
    """
    application = Application.builder().token(telegram_api_token).build()

    application.add_handler(CommandHandler("start", start))
    application.add_handler(CommandHandler("clear", clear_history))
    application.add_handler(MessageHandler(filters.TEXT & ~filters.COMMAND, chat))

    # Run the bot until manually terminated
    await application.run_polling(stop_signals=None)

if __name__ == '__main__':
    try:
        import asyncio
        asyncio.run(main())
    except (KeyboardInterrupt, SystemExit):
        logging.info("Bot shutdown gracefully")
```

### Key Changes:

1. **Environment Variables**: Utilizes environment variables with `python-dotenv` to avoid hardcoding the API token.
2. **Error Handling**: Added error handling with detailed logging for better debugging.
3. **Graceful Shutdown**: Added handling for graceful shutdown via logging.
4. **Documentation**: Included comments and docstrings to explain the functionality of each part.
5. **Updated `python-telegram-bot` Usage**: Used `Application` instead of `Updater` to reflect the latest changes in the `python-telegram-bot` library version 20.

### Additional Notes:

- Make sure `python-dotenv` is added to your `requirements.txt` for managing environment variables:

  ```
  python-telegram-bot==20.0
  python-dotenv
  ```

- Replace the placeholder `model_client.get_response()` with your actual model client implementation to generate responses to user messages.

Implement these suggestions, and you'll have a more reliable and maintainable Telegram bot application.