Refactor the routine for creating apexFile

This change is to make it easier to add new fields to the struct.
transitiveDep field is added to distinguish apexFiles coming from
transitive dependencies of the APEX. We will later use the info to
reduce the size of bundled APEXes by replacing the transitive deps with
symlinks to the corresponding files in the system partition outside of
the APEX.

Bug: 144533348
Test: m

Change-Id: I283859f2f2f1b5cfb3025569f168ba8569b22bb9