Clean URL/.htaccess problems with multiple subdirectories

Question

I've inherited a large Drupal web site and now we're updating from Drupal 6 to Drupal 7. I cannot enable CleanURL for more than one subdirectory at a time! I think I've read just about every article on CleanURLs there is, and possibly my situation is unique, or maybe I'm going about things wrong?

We have a couple versions live on our web site using different subdirectories and databases. There are two sites total on one domain, each with a Drupal 6 "live" copy and a Drupal 7 "test" version on the host. They are organized as follows:

siteA_D6 -> example.com/
siteB_D6 -> example.com/siteB_D6
siteA_D7 -> example.com/siteA_D7
siteB_D7 -> example.com/siteB_D7

We want the subdirectories to work as I've listed them above, but eventually we will retire the D6 versions and redirect D7 to example.com/ and example.com/siteB

Currently, all 4 sites are accessible, but, CleanURLs only work on siteA_D6 (or example.com). Ideally we want to have CleanURL enabled on all of them, so that

http://example.com/test/arguments and
http://example.com/siteA_D7/test/arguments 

resolve to the "same" page in different versions, and we never see ?q=test/arguments in the address bar

Our shared-server web host considers this issue "beyond ordinary technical support"... can't blame them, I've been banging my head up against this wall for days now. I'd really appreciate a solution or just some pointers.

(.htaccess copied below)

Options All -Indexes

ErrorDocument 404 "This page was not found on this server"

RewriteEngine On
RewriteBase /

Options +FollowSymLinks

# Closing the back door
RewriteCond %{QUERY_STRING} (ch|php_code)=(.*)
RewriteRule (.*) ##pretend url here, it won't let me post "too many links"## [L]

# Block pharmaceutical hotlink chicanery
RewriteCond %{HTTP_REFERER} ^http://.*pharmacy [NC]
RewriteRule .*\.(jpe?g|gif|bmp|png)$ - [F]

# stuff to let through
# I have been commenting these out when testing new rules
RewriteCond %{REQUEST_URI} "/siteB_D6/" [OR]
RewriteCond %{REQUEST_URI} "/siteB_D7/" [OR]
RewriteCond %{REQUEST_URI} "/siteA_D7/"
RewriteRule (.*) $1 [L]

#this one redirects all requests from domain to new folder
RewriteCond %{HTTP_HOST} ^.*example.org$
RewriteCond %{REQUEST_URI}  !^siteA_D6.*
RewriteRule ^(.*)$ "site_A_D6/$1" [L]

<IfModule mod_suphp.c>
suPHP_ConfigPath /home/username
<Files php.ini>
order allow,deny
deny from all
</Files>
</IfModule>    

Answer 1

It seems that your .htaccess is custom made, first of all you should have a look at the one Drupal provides as you're missing some criticals rules like

<FilesMatch "\.(engine|inc|info|install|make|module|profile|test|po|sh|.*sql|theme|tpl(\.php)?|xtmpl)$|^(\..*|Entries.*|Repository|Root|Tag|Template)$">
  Order allow,deny
</FilesMatch>

Regarding your problem, I think you should change the RewriteBase condition like this:

RewriteBase /siteB_D6

for each of you subsite (make it matches the subdirectory where it's located).