refactor: decompose _do_run_file into compiler, state, and exception handlers

[bhagathkrishnacdac]

Description
This PR refactors _do_run_file to address cognitive complexity and improve code readability. The original monolithic configuration loader, which handled file reading, syntax translation, warning prompts, global namespace preparation, execution, and verbose traceback formatting in a single nested block, has been broken down into single-responsibility helpers.

Key Changes

• Decoupled File Processing:
  • _process_config_file handles syntax transformation and compilation via sugar.
  • _handle_syntax_error manages the specific formatting of compilation errors.
• Isolated Pipeline Gates: _prepare_pipeline_state orchestrates safety checks, pausing worker threads and prompting on non-empty pipeline resets.
• Declarative Environment Setup: _setup_execution_globals isolates the instantiation of global variables and dynamic module creators required for executing scripts securely.
• Cleaned Exception Handling: _handle_execution_exception separates python traceback-frame extraction and formatting to keep the execution pathway clean.