There are two cases of WP dealing with links:
- real files, which WP ignores and let server deal with
- permalinks, which WP handles and processes
These two aren’t really meant to intersect much. If you provide alternate index then web server will serve it, while WP ignores it.
It is hard to say what the proper way to wire this would be, without seeing it. Likely this should be properly integrated with theme you are using or at least enqueued and processed, using WP’s APIs.
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