My phpwiki 1.3.6 is using the default index.php?page=
format. My zip file has my modified HomePage. The
option to Merge the files appeared to have a hardcoded
phpwiki/PhpAdministration link, not the ?page= version.
Since the ?page= format works on all wikis, it would
make sense to fix this. I can't figure out where this
is, but I will post a followup if I can locate it.