member of multiple groups indicates a malformed project or loss of `compilerFlags`

We are looking to move away from pods. As part of the process, we care converting the pods to yml so we can generate Xcode project files. This is a precautionary step in case we ever want to be able to debug a pod.

I'm working on FBSDKCoreKit, which has one file which doesn't use ARC. However, I am having a difficult time getting it to work right.

It's either my syntax/ordering or perhaps a bug.

If I use this to define the sources

    sources:
      - path: ../Pods/FBSDKCoreKit/FBSDKCoreKit/FBSDKCoreKit/Internal_NoARC/FBSDKDynamicFrameworkLoader.m
        compilerFlags: "-fno-objc-arc"
      - path: ../Pods/FBSDKCoreKit/FBSDKCoreKit/FBSDKCoreKit
        includes: "**/*.[hm]"
        excludes: Internal_NoARC/FBSDKDynamicFrameworkLoader.m

I receive a warning like the following. The build will work, however.

2020-02-13 14:03:55.266 xcodebuild[4804:1782108] warning: The file reference for "../Pods/FBSDKCoreKit/FBSDKCoreKit/FBSDKCoreKit/Internal_NoARC" is a member of multiple groups ("FBSDKCoreKit" 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.

Note that I've gotten rid of the excludes and the same error message will result.

I tried to re-order, but ordering does seem to matter, since if I re-order like the following

    sources:
      - path: ../Pods/FBSDKCoreKit/FBSDKCoreKit/FBSDKCoreKit
        includes: "**/*.[hm]"
        excludes: Internal_NoARC/FBSDKDynamicFrameworkLoader.m
      - path: ../Pods/FBSDKCoreKit/FBSDKCoreKit/FBSDKCoreKit/Internal_NoARC/FBSDKDynamicFrameworkLoader.m
        compilerFlags: "-fno-objc-arc"

-fno-objc-arc will not be set.

Is my syntax incorrect? Or is this a case where xcodegen cannot properly handle it? Or do I just accept the warning and ignore it?

Start by reproducing the project generation with the two YAML sources variants and inspect the resulting Xcode project warning about duplicate group membership. Compare the generated project behavior with and without excludes; done means the malformed-project warning is resolved and -fno-objc-arc remains applied to FBSDKDynamicFrameworkLoader.m.