QtCreator 3.1.1 does not handle SIGQUIT correctly

[Gregor]

Since 3.1.1 QtCreator will only create a .user-file when it exits via Ctrl+Q. Before 3.1.1, the file was created at startup.
How can I send a signal to a running qtcreator to quit like the user pressed Ctrl+q so that a .user file is created?

Background:
I'm using QtCreator as an C-IDE for embedded software development on ARM-NONE-EABI platform.
My projects require to run a special compile.sh script instead of make all. For this, I wrote a SHELL script to start qtcreator to have it create a .user file. After qtcreator has created the .user-file, the script simply sends it a SIGKILL to shut down. This .user-file is then modified for proper project settings. Then qtcreator is started again and shows the correct project settings.
Since 3.1.1, this automatic configuration does not work anymore.

Is there another way to automatically configure a qtcreator project?