Rebuild pkgdown docs (incorporate TileDB branch dev->main)

[jdblischak]

• Rebuilds the docs to incorporate the changes from Update _pkgdown.yml logo link #794 and Fix nightly build by updating branch name from "dev" to "main" #797 via Rscript -e "pkgdown::build_site()" (I used my local R 4.4.2 with pkgdown 2.1.1 on Ubuntu 22)
• Longer-term the plan is to automate the building and deployment of the pkgdown docs (Consider moving the pkgdown process and docs to separate workflows, and update deployment #798), but this PR simply rebuilds them as before to meet the immediate needs of fixing the current website problems
• I also updated vignettes/introduction.md. I had thought this was the generated file, but in fact its corresponding .Rmd is generated by vignettes/Makefile