I couldn't help but notice that you recently posted a very similar question on StackOverflow: r - Bookdown generates index file with a chapter title instead of "index.html" when knitted - Stack Overflow
The current way you've done this is generally considered not-OK
From: FAQ: Is it OK if I cross-post?
Posting the same question to multiple forums at the same time is often considered impolite. We don't completely ban such cross-posting, but we ask you to think hard before you do it and to follow some rules.
Cross-post sparingly
Rather than post the same thing here and elsewhere from the get-go, post in one place at a time. Let enough time go by (think days, not hours) before you take your question somewhere else. Sometimes people at another site may suggest you post here if your question doesn't fit within the scope of the other site.
Always link to your other posts, and update everywhere with any solutions
No matter what your reason for cross-posting is, when you post here please be sure to link to your related post on the other site and keep both ends updated with any solution.