gen and fetch write the manifest as index.mf at the top of the tree.
check left out only the manifest file it was given, so given a URL, or a
manifest stored elsewhere, it reported that index.mf as not in the
manifest, and --no-extra-files failed a tree fetch had just verified.
check now drops that one report for index.mf at the top of the base
directory. A manifest that lists index.mf still has it checked, and
index.mf in a subdirectory or fetch's leftover .index.mf.tmp are still
reported. The change is in package cli, which owns the default manifest
name; the Checker in package mfer is unchanged.
Model: opus-5-5
sneak