I'm building a site using the Professional Website template.
I've made some changes to the index template, but the changes are only reflected in the Blog, About and Contact index pages. The change will not show up in the main index/homepage. I then deleted the homepage from the page listing (w/ the intent of pointing to a different page as home), but it still keeps getting published at the root level when I republish the site, even though it doesn't exist in my list of pages.
Where is this page being generated from? How do I alter or delete it's index template?
Reported on Movable Type 4.2

it's a mixture of a page and an index template. If you look at the page for it, it has a tag of '@home' and then the "main Index" template includes an mt:pages tag with tag="@home" on it.
So to edit the design you use the template and to edit the content you use the page.
the "page" archive template affects pages only and if you look at the right hand side of your MT screen when editing the home page, you will see it's being published to a page template file as well as to the "main index" template.
Thanks for your response!
What I don't understand is why MT keeps generating a root level index page which does not reflect any of the changes that I made to the header template (all other index pages reflect this change). I DELETED this page so that I could put my own index.html file at the root level (redirecting to a subfolder's index). But each time I publish, it overwrites my index with the original index file (with some ridiculous picture of a rooster that I can't get rid of). I deleted the mt:pages "@home" tag from the index template, but to no avail.
Any ideas???
I figured this out...
The header contained 2 tags, which were specifying instructions for the homepage which ran contrary to my other instructions for the index pages.
When I deleted both instances of this tag, the homepage behaved properly.
Thanks!