APK-in-APEX should set use_embedded_native_libs: true

So far, we automatically have embedded JNI libs for APKs in APEX, even
if use_embedded_native_libs was not set or set to false.

With this change, such APKs should explicitly set the property.

This is in preparation for an upcoming change for using different
dependency tags to JNI deps depending on whether they are embedded (thus
no install is needed), or not (thus installation to the partition is
needed).

shouldEmbedJni function now doesn't make use of the ApexInfoProvider
which is not available during deps mutator.

Bug: N/A
Test: m
Change-Id: I836171aacba19dbfa0e09f16a773ae498c56d60b