Fix 2 filtering problems in multi dex + main list.

- Classes in archives were added in all dexes.
- Adding resources could be done twice in non "strictNameCheck" mode
(when using BestEffortMainDexListFilter) if there was 2 secondary
dex.

(cherry picked from commit ad27e19691c6723a801b127f8802f5cdf4f44359)

Change-Id: I5cbc1b273518e868fdd3d642d50488ddcbec2af6
2 files changed