As of BBEdit 13.1, the HTML Tidy built-ins are back and you should use those instead. This gist is so old it refers to "OS X", c’mon!
If for some reason you are using this, note @ryanfrancesconi’s comment about the correct place to put the file when using sandboxed versions of BBEdit.
I believe it was removed due to Tidy not being updated, and having "ownership" issues. If you look at the Tidy webpage, there is a gap from 2008 to 2015 when it sat idle.