mashID runs local command-line tools on local files. It downloads databases from Figshare over HTTPS and verifies their MD5 against values stored in the package. It never sends data anywhere.
If you find a security problem, for example an unsafe handling of file paths or a way to make the downloader write outside its directory, please email duceppemo@gmail.com rather than opening a public issue. You will get an answer within a week.
Only the latest release is supported with fixes.