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Yes, the documentation on master doesn't exactly match what's on NPM, because master is the development version (So grep('-l') won't work with the current npm version!). Sorry for any confusion!
I'm going to close this, but feel free to reopen if I've misunderstood the problem.
The documentation on http://documentup.com/shelljs/shelljs is out of sync with http://documentup.com/shelljs/shelljs. Specifically the grep command options '-l' was added in 90569dc and npm hasn't been updated since.
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