Never list index.mf at the top of the tree in gen and freshen (closes #233)

fetch saves the manifest as index.mf at the top of the tree and refuses a
manifest that lists a file there. gen given --output, and freshen with its
manifest outside the base directory, listed such a file, so they wrote
manifests fetch would not take.

Both now leave out each file the manifest would list as index.mf: one at
the top of the tree, or a file given to gen by that name. The rule goes by
that path alone and looks up no file, so a symlink named index.mf never
hides the file it points to. index.mf in a subdirectory is still listed.
The scanner in package mfer gets an option to leave out files by the path
they would be listed by.

Model: opus-5-5

internal/cli/freshen.go

@@ -192,6 +192,12 @@ func (s *freshenScanner) walk(path string, info fs.FileInfo, walkErr error) erro
 		return nil
 	}
 
+	// Leave out a file listed as index.mf, at the top of the base
+	// directory, since fetch saves the manifest there, as gen does.
+	if relPath == defaultManifestName {
+		return nil
+	}
+
 	// Handle symlinks
 	if info.Mode()&fs.ModeSymlink != 0 {
 		realInfo, keep := s.resolveSymlink(path)