eclipseClasspathtask no longer merges classpath entries present in the classpath file. It replaces all classpath entries with the dependencies declared in the build script.
eclipseWtptask has been split into
ideaModuletask no longer merges libraries present in the module file. It replaces all libraries with the dependencies declared in the build script.
ideaModuletask only includes in the module those source directories which exist. It used to include all defined source directories.