Revert r36413 -- renaming of search files into 'search' subdirectory

Revert r36413 -- renaming of search files into 'search' subdirectory
The loss of specific names would create a visible name conflict; when you've got "MySQL.php" open, what the hell is it? Is it the DatabaseMySQL class? Some other random MySQL-related thing? Update.php is also confusing -- we have an update.php which is a command-line script.
Don't do these confusing names; there's no pressing functional need to move the files at all, but if you must move them at least keep their distinct names so I can find my code.