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e.g. Upload file "helloWorld.txt" and it says it's going to be renamed to "helloWorld.txt" (the 
same title).

PATCH for includes/SpecialUpload.php:

FIND:
if( $this->mUploadSaveName != ucfirst( $filtered ) ) {
  $warning .=  '<li>'.wfMsg( 'badfilename', htmlspecialchars( $this->mUploadSaveName ) ).'</li>';
}

REPLACE WITH:
if ( $wgCapitalLinks ) {
  $filtered = ucfirst( $filtered );
}
if( $this->mUploadSaveName != $filtered ) {
  $warning .=  '<li>'.wfMsg( 'badfilename', htmlspecialchars( $this->mUploadSaveName ) ).'</li>';
}

(or put the first bit further up, where $filtered is first defined.)