add a new cleanup function to run_snakefile.sh file and then call it as part of main() function

[DininduSenanayake]

this is to address #95

1. Added a new cleanup_files function that:

• Uses the existing logging function for consistency
• Performs the same checks as your cleanup script
• Returns success/failure status

2. Modified the main function to:

• Track workflow success with a boolean variable
• Only attempt cleanup if the workflow completed successfully
• Log the cleanup results

3. Added proper error handling and logging for the cleanup process

The cleanup will only run if:

• Both Snakefiles complete successfully
• FAILED_CONFIG is empty
• FAILED_DB has at most one file