Set default '^ot:unrootedTree' to force a choice

Setting this per-tree flag to true marks (if not found) means that a
tree's rooting is considered arbitrary until the curator asserts
otherwise. Which is annoying, but safer than trusting the incoming
rooting to be deliberate.
Remove study-level flag '^ot:notUsingRootedTrees'

This is deprecated in favor of tree-level flags '^ot:unrootedTree'.