extract_files: Support system/ prefixes

With support for 4 independent partitions now, we seriously
need to start putting /system blobs in their own directory.
Add support for file lists with system/ prefixes while
maintaining support for old file lists without it.

Also, TARGET_COPY_OUT_SYSTEM is a thing now, and all devices,
regardless of treble or not, set TARGET_COPY_OUT_$partition
so let's get rid of the treble compat option and default it
to true.

Change-Id: I5b798d293768d7c1e16db3ba01e2de3e083088d7