Removing core from all files which could use an alternative.

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 un-used import (there were a lot)

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