you can add this in "Exclude URLs" option:
I could, but as most of the site structure relies on links present in each index file, that results in only a few 'siewide links' appearing in the XML Sitemap.
This is no solution.
I also tried experimenting with listing an actual URL, but it looks like the Exclude URLs option only matches strings, not entire URLs. In any case, this would have had the same effect.
It looks like the problem is the index.php and the folder are equivalent.
I then thought about the robots.txt file, but as far as I know - it only lets you remove folders or files.
I needed more control, and the only thing I have found that will allow this to work is a command in the HTML head section.
<meta name="robots" content="noindex">
This works, in that it does not create a link for the index file itself, however it does create them from links in the file.
If I had have used the following meta, not even the links inside the file would have worked...
<meta name="robots" content="noindex,nofollow">
Hope this helps someone else.
Any moderators listening, it would be nice to have this feature inside the sitemap generator, but I have no idea if sitemap standards support it anyway.