1. create simple "hello world" qbs project.
2. placed in /home/mapron/qt/ :
-qbs file
-two cpp files
3. compiled the last trunks from git qbs and QtC (2.8 branch).
4. run qbs from command line build, then clean. all ok
5. open project qbs in QtC (run with QBS_LOG_LEVEL=4), build, then clean - clean failed (and trying to delete some another IMPORTANT dirs, which IS NOT created by QBS):
DEBUG: Removing '/home/mapron/qt/diplom_server/files/steal/generate/templates/app/test'.

I have dig some more info:
-it is really removes files just as cmd version. But info messages are wrong. It was scaring for me...

So not so urgent, but should be fixed, i think.