test: replace indexOf with includes

Start the transition to Array.prototype.includes() and
String.prototype.includes().  This commit refactors most of the
comparisons of Array.prototype.indexOf() and String.prototype.indexOf()
return values with -1 to the former methods in tests.

PR-URL: https://github.com/nodejs/node/pull/12604
Refs: https://github.com/nodejs/node/issues/12586


Reviewed-By: Alexey Orlenko <eaglexrlnk@gmail.com>
Reviewed-By: James M Snell <jasnell@gmail.com>
Reviewed-By: Gibson Fahnestock <gibfahn@gmail.com>