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/gen.go

@@ -137,6 +137,9 @@ func (mfa *CLIApp) buildScannerOptions(
 		// Neither a manifest being replaced nor a temp file left by an
 		// interrupted run belongs in the new manifest.
 		ExcludePaths: []string{output, manifestTempPath(output)},
+		// Nor does a file listed as index.mf, at the top of the tree, since
+		// fetch saves the manifest there and refuses a manifest that lists it.
+		ExcludeRelPaths: []mfer.RelFilePath{defaultManifestName},
 	}
 
 	// Set seed for deterministic UUID if provided