I am developing a series of sites (for multi language purposes) installed with one instance of Wordpress in the server root, then further instances in country-code subdirectories. So there are installs at the following example URLs:
http://example.com http://example.com/en http://example.com/fr
The root directory install has a theme to deal with language detection and forwarding to relevant sub directory, as well as various other redirection functions.
The problem is that when trying to access a "pretty" permalink on one of the sub-installs, eg http://example.com/en/page-name, Apache intercepts and serves a 404 before the subdirectory install gets a chance to decipher and redirect the permalink. The odd thing is that on my localhost dev setup (MAMP), this setup works fine and these links resolve to the correct pages on the subdirectory WPs.
This site is on AWS running Amazon Linux AMI release 2014.03. I suppose the question is essentially, is it possible to stop Apache trying to deal with 404s within certain subdirectories and leave this entirely to WP, or, some way of changing one of the .htaccess files to achieve similar. The suggestion at http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory#Using_a_pre-existing_subdirectory_install won't work due to WP also being installed in root.