refactor: prefer includes over indexOf

[jamesgeorge007]

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• The changes are appropriately documented (if applicable).
• The changes have sufficient test coverage (if applicable).
• The testsuite passes successfully on my local machine (if applicable).

Summarize your changes:
Use includes() over indexOf() to check for existence.

[malept]

If you're going to make minor refactors, can you replace all of the usages of indexOf that you can and run the testsuite to make sure it's not going to break anything?