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This is on XCode 8.2, using CMake 3.8.1 and the XCode generator.

If a .swift file is included in the CMakeLists project, it is not included as part of the PBXSourcesBuildPhase. For example, I have two .swift files, AppDelegate.swift and ViewDelegate.swift. This is the PbxSourcesBuildPhase generated by cmake (edited to remove anything proprietary):

            3EF8DE5AF7E6448FBE1C4A89 /* Sources */ = {
                    isa = PBXSourcesBuildPhase;
                    buildActionMask = 2147483647;
                    files = (
                            2FF6DFE4F36F4C36A4FBBA91 /* Cardreader.mm */,
                            E53F580BD73F46C58233D5D4 /* main.mm */,
                    );
                    runOnlyForDeploymentPostprocessing = 0;
            };

After I manualy add the files to the target:

            3EF8DE5AF7E6448FBE1C4A89 /* Sources */ = {
                    isa = PBXSourcesBuildPhase;
                    buildActionMask = 2147483647;
                    files = (
                            3B71D98C1ECE9683007AA9DA /* ViewController.swift in Sources */,
                            3B71D98B1ECE967F007AA9DA /* AppDelegate.swift in Sources */,
                            2FF6DFE4F36F4C36A4FBBA91 /* Cardreader.mm in Sources */,
                            E53F580BD73F46C58233D5D4 /* main.mm in Sources */,
                    );
                    runOnlyForDeploymentPostprocessing = 0;
            };