I am aware of the MSApp.execUnsafeLocalFunction problem when it comes to DOM manipulation in jQuery, but even a modified version of jQuery link here fails verification with the Windows store.
It seems the pattern here is that all my Nuget pulled scripts fails verification. Anybody figures why?
Error Found: The bytecode generation test detected the following errors:
File \\?\C:\Program Files\...\Scripts\require.js has JavaScript syntax or other problems.
File \\?\C:\Program Files\...\Scripts\r.js has JavaScript syntax or other problems.
File \\?\C:\Program Files\...\Scripts\knockout-2.2.0.js has JavaScript syntax or other problems.
File \\?\C:\Program Files\...\Scripts\knockout-2.2.0.debug.js has JavaScript syntax or other problems.
File \\?\C:\Program Files\...\Scripts\knockout.mapping-latest.js has JavaScript syntax or other problems.
File \\?\C:\Program Files\...\Scripts\knockout.mapping-latest.debug.js has JavaScript syntax or other problems.
File \\?\C:\Program Files\...\Scripts\jquery-1.8.3.js has JavaScript syntax or other problems.
Try saving your files with the UTF8 byte-order mark (BOM) encoding. I had a similar issue and that solved the issue.
http://msdn.microsoft.com/en-us/library/windows/apps/hh849088.aspx
Not specific to your issue, but bytecode caching.
HTH