i've created a new project and added jQuery just like that:

<script src="js/jquery-1.8.2-win8-1.0.js"></script>

and i have error on exit of application.
'WWAHost.exe' (Script): Loaded 'Script Code (MSAppHost/1.0)'.
Exception was thrown at line 5357, column 6 in ms-appx://9639c33e-1eba-439f-9f8f-33d29838c67b/js/jquery-1.8.2-win8-1.0.js
0x800a139e - JavaScript runtime error: SyntaxError
The program '[3500] WWAHost.exe' has exited with code 1 (0x1).