Hi,
I tried searching for the same issue but couldnt find the right answer for me.
Anyway, I have a site http://mysite.com but the index.php from the root is going to redirect to a subfolder say, http://mysite.com/pages/index.php and on google webmaster tools fetch as googlebot i get the document moved message. And no indexing seems to be produced. But when manually adding the url for fetching say http://mysite.com/pages/?!page=home i get the results i expected.
My concern would just be if I can leave how i structured my site (redirect to pages subfolder for the main index) and this wont affect googlebot? i think my current site structure works well in my case to have a better orginzation of files.
Any help greatly appreciated. Thanks in advance!