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
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