I have just done a fresh install and there are heaps of files missing??

cache_public;
media/app;
media/images/classifieds;
plugins/htmlpurifier/standalone/HTMLPurifier/DefinitionCache/Serializer;
plugins/htmlpurifier/standalone/HTMLPurifier/DefinitionCache/Serializer/HTML;
plugins/htmlpurifier/standalone/HTMLPurifier/DefinitionCache/Serializer/CSS;
plugins/htmlpurifier/standalone/HTMLPurifier/DefinitionCache/Serializer/Test;
plugins/htmlpurifier/standalone/HTMLPurifier/DefinitionCache/Serializer/URI;
see more flash/modules/board/files;
flash/modules/chat/files;
flash/modules/photo/files;
flash/modules/im/files;