Well PUPs are potentially unwanted programs, a term invented by MacAfee's to keep them apart from general malware, these files can be classified as riskware and are malware only then when they have landed onto your computer unintentionally, so you have not installed the tool yourself or intentionally or it came bundled with another program or was placed there by a hacker for malicious purposes. It could be compared to a hammer, that can be either used to sculpt and beautify or to ruin and destruct. So you are the best judge as to exclude it or remove it and to decide on the status of it. The flag was only to warn you about the nature of the tool, executable, program, file...
polonus