Support multiple <application> or <uses-sdk> elements in manifest_*.py

Manifests may now have multiple copies of elements if they are
disambiguated with android:featureFlag attributes.  Remove the
restrictions on duplicate elements from manifest_check.py and
manifest_fixer.py, and instead iterate over all matching elements.

Test: manifest_check_test.py, manifest_fixer_test.py
Bug: 365170653
Flag: EXEMPT bugfix
Change-Id: Ib577439d03a808a20a5fcc3e15a3117e0970d729