qdoc loads index files in -prepare phase

qdoc clears the output directory in the -prepare phase, but only for the module it is running on. It doesn't clear the output directories for the other modules. This means that the index files for the other modules still exist, and qdoc reads them in the -prepare phase, because the "depends" list tells qdoc they are needed. I think qdoc should simply ignore the depends list in the -prepare phase. It should at least not load any index files in the -prepare phase.