#472 Update CIF to CIF transformations to not use OutputProvider.

• Best to review per commit.
• No end-user visible changes.
• Changes:
  • Removed application framework as dependency of the cif2cif plugin.
  • Updated CIF to CIF transformations to not use OutputProvider. Instead, they now get a WarnOutput-typed field that gets filled via a constructor parameter.
  • All instantiations of such CIF to CIF transformations now pass a relevant argument. They all already had one in scope to use directly. No need to forward it from their applications.
  • LinearizeMerge: Removed an unnecessary fmt call. WarnOutput.line supports formatting already.

Addresses #472