Thread:Project:Support desk/Short URL setup leaves some index.php links behind/reply (2)

Those were all links that can be found on any MediaWiki page, basically.

By default, the login and logout links are at the top right of the page, the printable version and permalink links are in the side pane on the left and the search (technically a form, not a link) can also be found at the top right.

RewriteRules have nothing to do with this, after all they cannot change the links that MediaWiki produces.