If you have a .qmlproject file specified as follows, the project explorer tree widget will collapse the qmlfiles/ directory when files are added into it through the filesystem. The tree works fine if qml files do not reside in subdirectories such as in this case, because the root node of the tree seems to be always open.

import QmlProject 1.0
Project {
QmlFiles

{ directory: "./qmlfiles" }

JavaScriptFiles

{ directory: "./qmlfiles" }

ImageFiles

{ directory: "./qmlfiles" }

}