Create a new project of type "Qt Quick Application - Empty" using Creator's wizard. For "Create in", select a directory inside an existing git checkout.
You'll get an error message like:

The wizard failed to generate files.
The error message was: "Cannot open D:\dev\64\MSVC2015\creator-4.5-nowebengine\share\qtcreator\templates\wizards\projects\qtquickapplication\empty\..\git.ignore for reading: No such file or directory".

The given path is inside the build directory of the running Creator, not inside the project directory you selected.

It should be possible to create projects inside a git repository. With Creator 4.4, this worked fine.

Found when updating Squish test tst_qtquick_creation.