Move hidden API encoding after resource merging

Previously, the hidden API encoding was done before resource merging.
However, hidden API modularization requires that the encoding be done
by the bootclasspath_fragment/platform_bootclasspath modules which will
be after the resource merging. Therefore, this change moves the hidden
API encoding after to match the future behavior.

It also moves the initHiddenAPI() method call after resource merging
too and passes it the result of the resource merging so it is available
for the bootclasspath modules via bootDexJar().

Although the resource merging was not always done when it was done it
would reorder the entries in the generated jar to match java ordering,
which puts the MANIFEST.MF first. This change preserves that behavior
by adding -j to the call to MergeZipCmds. This does mean that jars
which did not require resource merging now have a different order but
as both orders work that is not a significant change.

Bug: 179354495
Test: m com.android.art com.android.ipsec com.android.os.statsd com.android.conscrypt
      - verify that apart from the ordering change in the jars that this does
        not change the contents of the apex files
Change-Id: If74baad5659301ca6ca9c0f6484374420dda8c34