Warning for absent custom-setup stanza is shown multiple times

[duog]

General summary/comments (optional)

The new absent custom-setup stanza warning is shown for each of the configure, build, haddock, copy/register steps.
It is shown twice for the copy/register step when it triggers on a dependency. I haven't included the reproduction for this double appearance.

Steps to reproduce

1. clone https://github.com/duog/stack-bug. This contains a stack.yaml that has a single location, the semigroupoids commit:https://github.com/ekmett/semigroupoids/tree/d5605e9c3773bad14f922e6e65ba13785edfa7e0

2. output from stack build --haddock --verbose is in the repo in the file output, link

Expected

A single warning is present in output:
Package semigroupoids uses a custom Cabal build, but does not use a custom-setup stanza Not using the explicit setup deps approach based on configuration Strongly recommend fixing the package's cabal file

Actual

the warning appears 4 times.

Stack version

$ stack --version
Version 1.2.0, Git revision 241cd07d576d9c0c0e712e83d947e3dd64541c42 (4054 commits) x86_64 hpack-0.14.0

Method of installation

• Official binary, downloaded from stackage.org or fpcomplete's package repository

[mgsloan]

Thanks for the report! Duplicate of #3034 , which is resolved in the master version of stack (fix not yet in a released version)