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The per-file scanner discovery no longer (but probably already for a long time) identifies files that are part of the build. The indexer uses CoreModel.isScannerInformationEmpty(..) to determine whether a file is part of the build or not. (That's the only purpose of this method. The name is not well chosen but was never changed because it is API). Independent of whether the scanner discovery has discovered a file or not this method returns false. This makes the per-file scanner discovery much less useful.