What do I have to do to make ‘toggle comments’ work with my language? I assume it is some part of the syntax, but couldn’t find it easily looking at other languages.
You need to specify
editor.commentStart and optionally
editor.commentEnd (if your language needs it) in your package’s scoped-properties.
'.source.js': 'editor': 'commentStart': '// '
How do I go about doing this with the current version of Atom?
It is still the same as above. The file just moved in the repository. You can see it at its new location here.