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.
Note for others arriving here: if it's a sandboxed version of BBEdit, this location won't exist and instead will be:
~Library/Containers/com.barebones.bbedit/Data/Library/Application Support/BBEdit/Text Filters
They have a short cut from the Folders menu.