Removing WP Super Cache breaks Multisite and .htaccess

I had issues with WP Super Cache continuing to cache the wrong Homepage under a Multisite installation. I cleared the cache, tried the “Extra Homepage checks” checkbox, preload the cache, etc, it still happened eventually, showing anonymous users the homepage of the main site, not the homepage of the site being visited. Subpages and posts displayed fine. Anyways… so, I remove WP Super Cache, and it makes modifications to .htaccess to remove the plethora of mod_rewrite lines it requires to work. In doing so, it stripped out lines that make Multisite work. I tried resaving the permalinks, but it wouldn’t rewrite the correct .htaccess file.

So for anyone with the same problem, where removing WP Super Cache breaks multisite and all subpages return 404 errors, or images no longer display, here’s the default .htaccess file I found that fixes the site:

RewriteEngine On
RewriteBase /
RewriteRule ^index.php$ – [L]

# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ – [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*.php)$ $2 [L]
RewriteRule . index.php [L]

http://wordpress.org/extend/plugins/wp-super-cache/