cli.js has this line:
const files = args.filter(file => /\.(ts|tsx)$/.test(file))
This is incorrect - it doesn't support cts or mts files. It also doesn't work with js/cjs/mjs files with checkJs turned on.
Should be something like const files = args.filter(file => /\.(c|m)?(j|t)sx?$/.test(file))