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Keeping core API dependencies to a minimum

Marek Szuba requested to merge feature/nocore into master

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.

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