Update index.php to serve static files with query strings.

Trim off the query string before attempting to locate the file on the
filesystem. Thanks to Marko Marković for the initial patch.

Fixes #3910
Update ServerShell to use provided documentRoot.

Fix ServerShell from using the wrong path to the routing script when
a custom document root is used. Thanks to Marko Marković for the patch.

Fixes #3909
Don't use inline assignment.

CakePHP generally avoids inline assignment as it can be confusing and do
the wrong thing.