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I tend to find out about unique OS X terminal commands piecemeal. As problems arise, or as I read askdifferent, I'll find out about handy things like mdls and mdfind.

Is there a place that lists all the unique OS X commands and gives me an overview of what they do?

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Check out the Unix Commands Unique to Mac OS X / Darwin page by Matisse Enzer. It's not current (OS X 10.4.2, August 2005), but it's pretty good.

Edit: @bmike said to me things sure have changed since 10.4 so here's hoping he's got a more up-to-date resource! :)

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ss64 has an ok quick list, but it omits many of the Apple-specific commands such as networksetup.

I also learned a lot from the Wicked Cool series, though I'm not sure how up-to-date that is (probably more recent than 2005).

Shell scripting and programming in any of the most common languages (perl, python, ruby etc) is just a form of writing, and good writers borrow; great writers steal. Copy and paste, run it yourself, kick it and take it apart and learn how it works.

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