Fix missing site upgrade in upgrade-version script

* upgrade-version.pl
 * Include site directory in updates
 * Reformat tabs for spaces
 * Be a little less destructive with respect to spacing in pom.xml files.
   Rather than reprint version line with arbitrary tab prefix, rather
   extract and replace the actual version number only.

Cherry-picked from commit 13f1104920954b577177e08d72727a02ac4fe629
Upgrade site's pom version to 8.4.1