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This handy set of rules for mod_rewrite automatically redirects any URL ending in "/index.php" to the same URL ending in "/."  It works for the root directory as well as subdirectories.

RewriteCond %{THE_REQUEST} ^GET\ /.*/index\.(php|html)\ HTTP
RewriteRule (.*)index\.(php|html)$ /$1 [R=301,L]

For example, "http://www.example.com/subdirectory/index.php" would be redirected to "http://www.example.com/subdirectory/."

This eliminates one of the peskier canonicalization issues with relative ease.  It's a bit tricky because of the way mod_rewrite updates its variables during execution — hence the odd use of the variable {THE_REQUEST}.  If anyone knows an easier way or finds a problem with it, leave a comment.