Windows users want to use the file from the download link above.
Linux/macOS users will want to download this file (make sure to make it executable before you try and run it). Note that Linux and macOS users also need to ensure perl is installed on their system, and the following may also be required to satisfy dependencies (run from a terminal):
cpan install Config::IniFiles
On Linux there is a chance your package manager will provide this, so check there for
perl-Config-IniFiles or a similar package first.
tes3cmd clean --help for detailed information about how the program cleans.
The official wiki and this reddit post about using
tes3cmd.exe with MO2 on Windows are great resources.