Handle verify-profile and bootclasspath classes in vdex.

Two problems:
1) An apk might define a class twice, or define a class that
   is already in the bootclasspath, or define a class that
   in the future happens to be in the bootclasspath.
2) verify-profile does not make classes that were not verified
   as verify-at-runtime for vdex.

Fixes:
1) Check that the resolved class is part of the dex file that
   we are currently looking into. If not, don't update its
   verification status.
2) Make unverified classes as such when they are not in the profile.

bug:34108532
Test: 634-vdex-duplicate
Change-Id: I77c5e417c16c91af257b88b6456d07c0e4c2ca93