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"file reference member of multiple groups" warning in Xcode 10 #405

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@LinusU

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@LinusU

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

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