We cannot set xref3 data without the `xnum' column to
tie it to the per-inbox over.sqlite3 DB. So ensure we don't
read brand-new history that only exists in git, but instead
rely on last_commit and last_xap15-$EPOCH metadata in msgmap
to decide how far we can index.
Before this change, it was possible to miss messages in
the extindex if -index did not run (which will be fixable by
upcoming --reindex support in -extindex).