Add custom library header save/restore code.

Should migrate current 1.12 installations from the old QT binary blob
to the new protobuf format.  This won't help us for users upgrading
from 1.11, but all future upgrades should be much smoother.
includes a small roundtrip test.

Add a comment about whether this is a logical index, a visual index, an index in the header_state repeated field, etc.?