XcodeGen regen can break a hand-kept pbxproj: 'member of more than one group'

In a repo whose project.pbxproj is committed but has drifted from project.yml, running xcodegen generate (2.46.0) to pick up new Swift files produced a project xcodebuild refused to open: 'The reference "shared-with-app" is a member of more than one group'. Safer for a few new files: git checkout the pbxproj and add PBXBuildFile, PBXFileReference, PBXGroup and Sources-phase entries by a small script anchored on an existing sibling file's lines, then plutil -lint. Separately, a symlinked folder holding an .xcframework gave 'There is no XCFramework found at ...'; an APFS clone copy (cp -Rc) plus deleting the derived-data folder fixed it.