Write gen DIR's manifest to DIR/index.mf (closes #178)

Without --output, gen given one directory now writes index.mf in it,
and given one file writes index.mf beside it; with no path or several,
it still writes index.mf in the current directory. What gen lists
depends only on its arguments and the tree, never on where the manifest
is written, so gen DIR followed by check DIR passes.

Scanner.EnumeratePaths lists a file argument by its name, as
EnumerateFile does. Before, it listed the file under an empty path and
gen stopped with "path cannot be empty".

The --output help text and the README's Tool Examples state the default.

Model: opus-5-5

internal/cli/mfer.go

@@ -211,9 +211,10 @@ func (mfa *CLIApp) generateCommand() *cli.Command {
 			},
 			&cli.StringFlag{
 				Name:    "output",
-				Value:   defaultManifestName,
 				Aliases: []string{"o"},
-				Usage:   "Specify output filename",
+				Usage: "File to write the manifest to (default: index.mf in " +
+					"the directory given, or beside the file given; with no " +
+					"path or several, index.mf in the current directory)",
 			},
 			&cli.BoolFlag{
 				Name:    "force",