Quote: "quick question: ./obj/ doesn't the . go back one directory?"
No, a single period means the current directory. '..' means the one above.
The CoreForApp.h and Core.cpp files are platform specific things.
I have not tried to use the batch file method in v1076. I updated the Wiki page to use that instead of the instructions for setting the permissions on everything.
Try using the original cygwin instructions for navigating to your project directory and doing the clean and build.
Or, here are cygwin instructions for making everything writable/owned by your Windows id:
cd /cygdrive/c/Android
chown -R <winusername>:mkgroup *
chmod -R a+r,a+w *
That might clear up the problem.
Cheers,
Ancient Lady
AGK Community Tester and AppGameKit Master