As we have continually extended utils.py it has become worthy of a refactor due to the immense technical debt. Since utils is a catch-all concept, we should split it up into a module. This refactor should be done in steps

1. Move all current utils.py classes and functions to a new utils submodule, such as utils/files.py
2. Change functionality of existing classes and functions to be less dependent on other modules to prevent circular dependencies
3. Possibly rename utils to a different name or further split the utils into more separate modules