Keeping core API dependencies to a minimum

Created by: andrewyatz

It seems we have others within the team that would like to use ensembl-io but will not because of the core dependency. This commit attempts to

1. Remove any use of Utils::Exception and replace it with Carp
2. Remove any use of Utils::IO work_with_file and replace it with an open
3. Remove any unused/unnecessary imports (there were a lot)

Also this commit pulls up that simple_list.t is no longer a valid test because its dependencies are broken.