Flatten the VFS subpackages

This allowed to make some classes and methods package-visible only.

(cherry picked from commit 7df4301ae2e2dd074235bd97d60bdd169e9ba085)

Change-Id: Ia3ff4dc630f910f0a4fcd14de22fc913a492c5bf
-o option is no longer a file but a folder

Change-Id: I46702a101e0d42015943e34e91008cd9a18331c6
Merge dex writers and always use ResourceWriter

Change-Id: I654bb9ce9a1af2a990172ed9164ec28d2a420ad0