metadataonlyctx: don't crash when reusing the manifest with deletions
This was originally fixed by Mateusz Kwapich for the `metaedit` command in
fb-hgext with a test for the `metaedit` command. It didn't get upstreamed
because `metaedit` was not in core.
This patch fixes the crash and adds a test about `metadataonlyctx` to
avoid future regressions.
Differential Revision: https://phab.mercurial-scm.org/D550