Set threads' contextClassLoader during LoadedApk.makeApplication.

We used to set this from LoadedApk.getClassLoader. This had
the unfortunate side effect of clobbering the threads default
classloader when Context.createPackageContext().getClassLoader()
was called. This happens, for example, to every app that uses
a updatable webview.

bug: 17986934
Change-Id: If2b5938a19f836ea5fe60c94ea53a7125c2098c0