qdoc has always stored all C++, QML, and other documentation in a single tree. Even the data loaded from index files is stored in the singleton tree structure.

qdoc should build a separate tree for each index file it reads, and there should be a separate tree for the current module, i.e. for all the C++, QML, and other documentation read from .h, .cpp, .qml, and .qdoc files.