manifest: disallow setting the node id of an entry to None
manifest.diff() uses None as a special value to denote the absence of
a file, so setting a file node to None means you then can't trust
manifest.diff().
This should also make future manifest work slightly easier.
context: stop setting None for modified or added nodes
Instead use a magic value, so that we can identify modified or added
nodes correctly when using manifest.diff().
Thanks to Martin von Zweigbergk for catching that we have to update
_buildstatus as well. That part eluded my debugging for some time.