"file reference member of multiple groups" warning in Xcode 10

After upgrading to Xcode 10, I'm getting the following warning when building my project:

2018-09-19 13:29:32.267 xcodebuild[17317:5682171] warning:  The file reference for "Sources/Components" is a member of multiple groups ("Sources" and ""); this indicates a malformed project.  Only the membership in one of the groups will be preserved (but membership in targets will be unaffected).  If you want a reference to the same file in more than one group, please add another reference to the same path.
2018-09-19 13:29:32.267 xcodebuild[17317:5682171] warning:  The file reference for "Sources/Coordinators" is a member of multiple groups ("Sources" and ""); this indicates a malformed project.  Only the membership in one of the groups will be preserved (but membership in targets will be unaffected).  If you want a reference to the same file in more than one group, please add another reference to the same path.
2018-09-19 13:29:32.267 xcodebuild[17317:5682171] warning:  The file reference for "Sources/Extensions" is a member of multiple groups ("Sources" and ""); this indicates a malformed project.  Only the membership in one of the groups will be preserved (but membership in targets will be unaffected).  If you want a reference to the same file in more than one group, please add another reference to the same path.
2018-09-19 13:29:32.287 xcodebuild[17317:5682171] warning:  The file reference for "Sources/Pages" is a member of multiple groups ("Sources" and ""); this indicates a malformed project.  Only the membership in one of the groups will be preserved (but membership in targets will be unaffected).  If you want a reference to the same file in more than one group, please add another reference to the same path.
2018-09-19 13:29:32.287 xcodebuild[17317:5682171] warning:  The file reference for "Sources/Stores" is a member of multiple groups ("Sources" and ""); this indicates a malformed project.  Only the membership in one of the groups will be preserved (but membership in targets will be unaffected).  If you want a reference to the same file in more than one group, please add another reference to the same path.

My directory structure looks like this:

Sources/
  Components/
    *.swift
  Coordinators/
    *.swift
  Extensions/
    *.swift
  Pages/
    *.swift
  Stores/
    *.swift
  *.swift
project.yml

Start by reproducing the Xcode 10 warning with the project.yml structure shown in the issue and inspect the generated project’s group references. Confirm the generated project no longer reports duplicate group membership while preserving target membership, then verify the warning is absent from the xcodebuild output.