It can handle sources in subdirectories it is because you have some Makfiles in the subdirectories with notations for QtCreator(win) and these can not be analysed from autobuilder.
So you need to change your rules file like this from the wiki.

Maybe that helps some people who are struggling with the same.

Instead of commenting out the "make clean" command you can put another command above.

And the makefile gets created in the autobuilder and will have some linux format which will not cause Multiple Target Patterns when a make command is called.