Fix missing class detector to work for incremental manifest edits

The missing manifest detector provides multiple issues; both the
missing class detector (which requires not just manifest scope but
also class scope), as well as some checks to ensure that for example
inner classes are registered correctly, which only requires manifest
scope. Because of this second issue, the detector runs in incremental
manifest editing context, but the code to handle missing classes would
also run. The check is simple; don't check missing class references
unless we also have class scope.

Change-Id: Iff83c372abf2335e3d8e991740702d6094fd65bd