manifest: repurpose flagsdiff() into (node-and-flag)diff()
The manifestdict class already has a method for diff flags between two
manifests (presumably because there is no full access to the private
_flags field). The only caller is merge.manifestmerge(), which also
wants a diff of files between the same manifests. Let's combine the
code for diffing files and flags into a single method on
manifestdict. This puts all the manifest diffing in one place and will
allow for further simplification. It might also be useful for it to be
encapsulated in manifestdict if we later decide to to shard
manifests. The docstring is intentionally unclear about missing
entries for now.
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