I'm not sure if this warning is ever relevant or safe to suppress, but I have ignored it for my whole Haskell maintainer life.

Warning: Cannot run preprocessors. Run 'configure' command first.

However, this is surely confusing to a newbie. Especially if they end up using stackage configure:

$ stackage configure
Invalid argument `configure'

Usage: stackage [--help] [--version] [--summary] COMMAND
  Run stackage commands

PS: Is there a paper cut tag for tooling issues? :)