v2: one file, really

We need to ensure there is only one file in the top-level tree
at any commit so the "add; remove; add;" sequence on the same
message is detected properly.

Otherwise, git will not detect the second "add" unless
a second message is added to history.

Deletes are now stored in "d" (and not "D" or "_/D") at the
top-level, now.  There's no need to have a "_" to reduce churn
as "m" and "d" should never co-exist.  It's now lowercased to
make it easier-to-distinguish from "D" in git-log output.

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