Fix serializing dynamic references to proto

The is_dynamic bit on references was getting lost when converting to
proto and back. This was preventing bundles from being used as shared
libraries, since layout inflation would fail when it hit a dynamic
reference.

Bug: 146491000
Test: Build a shared library with a layout that has a dynamic reference,
      and attempt to inflate that layout.

Change-Id: Ia0e615670d2ac52f9266e3eec8813af7687d3323