I would request for another file in the utils: gen-project.bat. All the other files are mac shell things, ( not counting the .py) so its time for something for windows.
I'm not fantastic with batch, but this is what i use:
set /p name= What do you want the call your project?
ECHO Generating Project...
XCOPY "Flixel\Project Template\*.*" %name%\ /e /i /f /h /y
ECHO Project Created!
THis generates a flixel project from a template in Flixel\Project Template. This is useful as a template can be easily customized, (for example, someone who always uses a Player class, or someone who puts everything in com.steve.mode) BUT because od that, you need a template. This could be included in the git download, but size might be an issue.
Anyway, feel free to put that in. You dont have to though.
Also feel free to modify/improve it. That will probably need to be done.