__ files are temporary files created by IntelliJ when safe write is enabled (Settings -> Appearance & Behavior -> System Settings -> Use "safe write").
Looks like the file has been deleted by IntelliJ between the time GWT has detected it was created (using Java watch service) and calling Files.isHidden(). Please open a bug for it.
To workaround it you can disable the above setting in IntelliJ which should prevent creating temp files on saving or you disable the file watching in GWT by adding -Dgwt.watchFileChanges=false to your run configuration.
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