Fix line endings

Set to Unix line endings in repo; the gitattributes file means they
will be converted to suit the user’s system.
Convert some files to tab indentation
Move page controllers into subdirectory
Replace old qa-page-* files with stubs

Simply call through to the new files, to maintain
backwards-compatibility.
Move language files into subdirectory
Replace old qa-lang-* files with stubs
Move AJAX controllers into subdirectory
Replace old qa-ajax-* files with stubs
Move native plugins into subdirectory
Replace old module files with stubs
Move qa-app-* files into subdirectory
Update all qa-app-* includes
Move qa-db-* files into subdirectory
Update all qa-db-* includes
Replace old qa-app-* and qa-db-* files with stubs
Move utility functions into subdirectory
Replace old qa-util-* files with stubs
Use plugins subdirectory for native modules/layers
Fix plugin stubs
Clean up and normalize all source code comments