Features
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- From now the scripts can use `command_file` instead of `command` to specify
  an external file from which the command template will be loaded. This makes
  it easier to manage larger scripts without cluttering `pelconf.yaml`.

Fixes
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- Fixed bug where if files collection defines `only_staged=True` and has non
  empty `include` list and none of the staged fiels match the `collect_files`
  function would pick all files (empty whitelist). Now it will correctly return
  an empty list (none of the staged files match the whitelist).