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.
Doxygen documentation update:
* Changed alls @addtogroup to @ingroup. @addtogroup adds the comment to the group description, but doesn't add the file, class, function, ... to the group like @ingroup does. See for example http://svn.wikimedia.org/doc/group__SpecialPage.html where it's impossible to see related files, classes, ... that should belong to that group.
* Added @file to file description, it seems that it should be explicitely decalred for file descriptions, otherwise doxygen will think that the comment document the first class, variabled, function, ... that is in that file.
* Removed some empty comments
* Removed some ?>
Added following groups:
* ExternalStorage
* JobQueue
* MaintenanceLanguage
One more thing: there are still a lot of warnings when generating the doc.
* Add @addtogroup tags to various classes, to try and group conceptually-related classes together.
* Add brief descriptions to various Special pages, thanks to Phil Boswell.
* Moving some docs to be right above the classes they represent, so that they are picked up.
