thanks for your reply.
i have another quick question -- though it is not particularly about the sitemap but rather it is about redirecting index.php to the root domain, as you suggest.
i have anchor links to sections in my home page and when i 301 redirect the index.html to the root (using RewriteRule ^index.php?$ /? [R=301] in the htaccess file), all of those anchor links within the home page break (you just land at the top of the home page).
those links from other pages in my site to certain sections on the home page look similar to this...
is it ok (as far as SEO) if i change those internal links to look like this?...
as far as the visitors' experience, i tested it and anchor links with absolute addresses without the index.php typed in the address work fine when i use that 301 redirect of the index page.