A 301 done properly will do exactly what you want. All ranking factors will be passed on accordingly to the 301'd page. (as long as you do it properly, this is not a tactic to rank new pages, only for 'moving' pages).
Google (and yahoo should) will follow the command of the 301 and consider all weight to the "Permanently Moved" url to the new url.
Save yourself some future grief, and never, link to the index.html, OR index.php. and link to the folder/directory. I wouldnt 301 it to the new index.php, I would 301 it to the sitename.com/ directory index. (then it wont matter what kind of index you use today, or in 10 years.
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